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This page was generated on 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbLipidmaps on palomino7

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: 1.10.0
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-10-16 23:18:07 -0400 (Wed, 16 Oct 2024)
EndedAt: 2024-10-16 23:21:32 -0400 (Wed, 16 Oct 2024)
EllapsedTime: 204.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biodbLipidmaps/DESCRIPTION' ... OK
* this is package 'biodbLipidmaps' version '1.10.0'
* 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 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 code 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 whether startup messages can be suppressed ... 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 3.51   1.74   46.57
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/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
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-10-16 23:19:45.804][biodb::testContext]
biodb.INFO [2024-10-16 23:19:45.808][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 23:19:45.809][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-16 23:19:45.810][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 23:19:45.812][biodb::testContext]
biodb.INFO [2024-10-16 23:19:45.819][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 23:19:45.822][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 23:19:45.830][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:19:45.832][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 23:19:45.833][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 23:19:45.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.838][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 23:19:45.871][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 23:19:45.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.876][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 23:19:45.877][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 23:19:45.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.881][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 23:19:45.883][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 23:19:45.884][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 23:19:45.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.888][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 23:19:45.889][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 23:19:45.891][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 23:19:45.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.896][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 23:19:45.897][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 23:19:45.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.902][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 23:19:45.903][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 23:19:45.904][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 23:19:45.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.909][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 23:19:45.910][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 23:19:45.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.914][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 23:19:45.916][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 23:19:45.917][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 23:19:45.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.921][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 23:19:45.922][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 23:19:45.924][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 23:19:45.925][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 23:19:45.926][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 23:19:45.927][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 23:19:45.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.932][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 23:19:45.933][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 23:19:45.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.937][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 23:19:45.939][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 23:19:45.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.942][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[2024-10-16 23:19:45.943][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 23:19:45.944][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 23:19:45.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.949][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 23:19:45.950][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 23:19:45.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.954][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[2024-10-16 23:19:45.955][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 23:19:45.956][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 23:19:45.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.961][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 23:19:45.963][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 23:19:45.966][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 23:19:45.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.971][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 23:19:45.972][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 23:19:45.973][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 23:19:45.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:45.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:45.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:45.980][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 23:19:46.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.021][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 23:19:46.023][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.024][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:19:46.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.028][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.030][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:19:46.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:19:46.033][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.034][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 23:19:46.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:19:46.036][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.039][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:19:46.039][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:19:46.039][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 23:19:46.039][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 23:19:46.039][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 23:19:46.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:19:46.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:19:46.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.047][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.048][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:19:46.056][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:19:46.058][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.059][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.060][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 23:19:46.062][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.063][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 23:19:46.065][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.066][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:19:46.067][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.068][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.069][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.070][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.072][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 23:19:46.073][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:19:46.074][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.075][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 23:19:46.076][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:19:46.078][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.079][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.080][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:19:46.080][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:19:46.080][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 23:19:46.080][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 23:19:46.080][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 23:19:46.081][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:19:46.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:19:46.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.088][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.089][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.090][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:19:46.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:19:46.093][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.094][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.095][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 23:19:46.097][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.098][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 23:19:46.099][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:19:46.102][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.103][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.104][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.107][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:19:46.108][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:19:46.109][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.110][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 23:19:46.112][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:19:46.113][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.114][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.115][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.116][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:19:46.118][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:19:46.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.124][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.126][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:19:46.127][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:19:46.128][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.129][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.130][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 23:19:46.132][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.134][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 23:19:46.135][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.136][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:19:46.137][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.138][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.140][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.141][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.142][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 23:19:46.143][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:19:46.144][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.146][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 23:19:46.147][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:19:46.148][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.149][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.150][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.152][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:19:46.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.155][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:19:46.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.159][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.161][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:19:46.162][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:19:46.163][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.164][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.168][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:19:46.169][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.281][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 23:19:46.286][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 23:19:46.294][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 23:19:46.296][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 23:19:46.298][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 23:19:46.299][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 23:19:46.301][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 23:19:46.302][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 23:19:46.304][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 23:19:46.306][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 23:19:46.307][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 23:19:46.309][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 23:19:46.310][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 23:19:46.312][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 23:19:46.313][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 23:19:46.315][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 23:19:46.316][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 23:19:46.318][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 23:19:46.320][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 23:19:46.321][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 23:19:46.323][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 23:19:46.324][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 23:19:46.326][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 23:19:46.328][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 23:19:46.330][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 23:19:46.332][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 23:19:46.333][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 23:19:46.335][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 23:19:46.337][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 23:19:46.340][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 23:19:46.343][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 23:19:46.345][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 23:19:46.346][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 23:19:46.348][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 23:19:46.349][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 23:19:46.351][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 23:19:46.353][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 23:19:46.354][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 23:19:46.356][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 23:19:46.359][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 23:19:46.361][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 23:19:46.363][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 23:19:46.364][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 23:19:46.366][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 23:19:46.368][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 23:19:46.370][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 23:19:46.371][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 23:19:46.373][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 23:19:46.374][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 23:19:46.376][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 23:19:46.379][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 23:19:46.382][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 23:19:46.384][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 23:19:46.387][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 23:19:46.390][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 23:19:46.392][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 23:19:46.395][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 23:19:46.397][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 23:19:46.400][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 23:19:46.402][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 23:19:46.405][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 23:19:46.407][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 23:19:46.409][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 23:19:46.412][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 23:19:46.414][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 23:19:46.417][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 23:19:46.419][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 23:19:46.422][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 23:19:46.424][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 23:19:46.427][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 23:19:46.430][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 23:19:46.432][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 23:19:46.435][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 23:19:46.437][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 23:19:46.440][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 23:19:46.442][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 23:19:46.444][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 23:19:46.447][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 23:19:46.450][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 23:19:46.452][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 23:19:46.455][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 23:19:46.457][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 23:19:46.460][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 23:19:46.495][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 23:19:46.499][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 23:19:46.503][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:19:46.505][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.509][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.610][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.DEBUG[2024-10-16 23:19:46.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.626][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[2024-10-16 23:19:46.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.634][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[2024-10-16 23:19:46.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.649][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[2024-10-16 23:19:46.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:19:46.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:46.660][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-16 23:19:46.669][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:19:46.671][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.672][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.673][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.675][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:19:46.676][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.677][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.678][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.679][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.681][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:19:46.682][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:19:46.683][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.684][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-16 23:19:46.686][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-16 23:19:46.687][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-16 23:19:46.688][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 23:19:46.689][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:19:46.689][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:19:46.691][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:19:46.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.694][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:19:46.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:19:46.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:19:46.697][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:19:46.698][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 23:19:46.698][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-16 23:19:46.700][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:19:46.701][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:19:46.702][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 23:19:46.703][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:19:46.709][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-16 23:19:46.710][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 23:19:46.732][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:19:46.734][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-16 23:19:46.738][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:19:46.742][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-16 23:19:46.747][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 23:19:46.749][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 23:19:46.752][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-16 23:19:46.753][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-16 23:19:46.767][biodb::testThat]
biodb.INFO [2024-10-16 23:19:46.769][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-16 23:19:46.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:46.771][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:46.791][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-10-16 23:19:46.795][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-16 23:19:46.800][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 23:19:46.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:46.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:46.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:46.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:46.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:46.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:46.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:19:46.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:46.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:46.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:46.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:46.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:19:46.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:19:46.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.909][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:46.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:46.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.915][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:46.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:46.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.920][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:46.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:46.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.963][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:46.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:46.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:46.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:46.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.980][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:46.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:46.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.988][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:46.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:46.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:46.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:46.996][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:46.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.035][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:47.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.043][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 23:19:47.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.066][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:47.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.209][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.217][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.232][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:47.276][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-16 23:19:47.286][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:19:47.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:19:47.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.295][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:19:47.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:19:47.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.303][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 23:19:47.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 23:19:47.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.309][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 23:19:47.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 23:19:47.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.373][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.416][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.421][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.426][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:47.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.470][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.472][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.476][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.521][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.525][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.578][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.580][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.584][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.609][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.623][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.628][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.633][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.670][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.671][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.673][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.690][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.705][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.706][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.708][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.709][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.725][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.726][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.729][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.736][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.738][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.743][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.754][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:47.756][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:47.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.760][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.771][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.778][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.789][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:47.791][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:47.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.795][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.811][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.812][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.815][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 23:19:47.828][biodb::testThat]
biodb.INFO [2024-10-16 23:19:47.830][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-16 23:19:47.831][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:47.832][biodb::testThat]
biodb.DEBUG[2024-10-16 23:19:47.846][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-10-16 23:19:47.853][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 23:19:47.863][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-10-16 23:19:47.865][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:47.869][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-10-16 23:19:47.871][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 23:19:47.906][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-16 23:19:47.908][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 23:19:47.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:47.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:47.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:47.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:47.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:47.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:47.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:19:47.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:47.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:47.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:19:47.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:19:47.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:19:47.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:19:47.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.951][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:47.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:47.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.956][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:47.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:47.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.961][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:47.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.971][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:47.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.982][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:47.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.987][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:47.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:47.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:47.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:47.993][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:48.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:48.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:48.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:48.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.035][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:48.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.042][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 23:19:48.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.066][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:48.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.105][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:48.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:48.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:48.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:48.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:48.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:48.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:48.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:48.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:48.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:48.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:48.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:48.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:48.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:48.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:48.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:48.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:48.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:48.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:48.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:48.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:48.181][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-16 23:19:48.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-16 23:19:48.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-16 23:19:48.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-16 23:19:48.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-16 23:19:48.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-16 23:19:48.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-16 23:19:48.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 23:19:48.219][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.221][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-16 23:19:48.223][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:48.225][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:48.230][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.233][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.237][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:48.239][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-10-16 23:19:48.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:48.305][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-16 23:19:48.310][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[2024-10-16 23:19:48.331][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:48.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-16 23:19:48.357][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:48.382][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-10-16 23:19:48.386][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-10-16 23:19:48.423][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:48.426][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:48.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.430][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 23:19:48.438][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.440][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-16 23:19:48.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:48.444][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:48.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:48.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:48.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:48.663][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[2024-10-16 23:19:48.667][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:48.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-16 23:19:48.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:48.673][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-10-16 23:19:48.715][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.718][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-16 23:19:48.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:48.722][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:48.755][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.762][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.768][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 23:19:48.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 23:19:48.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.773][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 23:19:48.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 23:19:48.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:19:48.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.845][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 23:19:48.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 23:19:48.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:48.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 23:19:48.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 23:19:48.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:48.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 23:19:48.875][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.876][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-16 23:19:48.877][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:48.879][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.901][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.903][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-16 23:19:48.905][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:48.907][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.927][biodb::testThat]
biodb.INFO [2024-10-16 23:19:48.929][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-16 23:19:48.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:48.933][biodb::testThat]
biodb.DEBUG[2024-10-16 23:19:48.940][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-10-16 23:19:49.733][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-10-16 23:19:50.416][biodb::testThat]
biodb.INFO [2024-10-16 23:19:50.419][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-16 23:19:50.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:50.423][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:50.435][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:50.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:50.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.439][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.440][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.442][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.444][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 23:19:50.446][biodb::testThat]
biodb.INFO [2024-10-16 23:19:50.448][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-16 23:19:50.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:50.451][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:50.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:50.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:50.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:50.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:50.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:50.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:50.617][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[2024-10-16 23:19:50.624][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:50.627][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-16 23:19:50.630][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:50.634][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-10-16 23:19:50.722][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[2024-10-16 23:19:50.726][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:50.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-16 23:19:50.729][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:50.731][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-10-16 23:19:50.765][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 23:19:50.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 23:19:50.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 23:19:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 23:19:50.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:50.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:50.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:50.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:50.854][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[2024-10-16 23:19:50.860][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:50.862][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359".
biodb.TRACE[2024-10-16 23:19:50.864][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:51.173][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content".
biodb.DEBUG[2024-10-16 23:19:53.338][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[2024-10-16 23:19:53.343][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:53.345][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3".
biodb.TRACE[2024-10-16 23:19:53.347][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:53.351][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content".
biodb.DEBUG[2024-10-16 23:19:53.405][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[2024-10-16 23:19:53.411][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:53.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54".
biodb.TRACE[2024-10-16 23:19:53.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:53.422][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content".
biodb.TRACE[2024-10-16 23:19:53.496][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 23:19:53.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 23:19:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:53.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 23:19:53.553][biodb::testThat]
biodb.INFO [2024-10-16 23:19:53.555][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-16 23:19:53.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:53.559][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 23:19:53.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 23:19:53.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:53.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:53.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 23:19:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 23:19:53.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:53.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:53.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:53.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:53.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:53.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:53.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:53.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:53.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:53.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:53.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:53.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:53.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:53.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:53.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:53.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:53.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:53.643][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[2024-10-16 23:19:53.650][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:53.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-10-16 23:19:53.654][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:54.022][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-10-16 23:19:56.437][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-10-16 23:19:56.512][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-16 23:19:56.516][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-10-16 23:19:56.519][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-10-16 23:19:56.547][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv".
biodb.DEBUG[2024-10-16 23:19:56.550][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 23:19:56.552][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-16 23:19:56.555][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 23:19:56.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:56.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:56.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:56.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:56.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:56.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:56.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:19:57.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:19:57.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:19:57.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:19:57.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:19:57.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.043][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:57.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:57.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.052][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:57.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:57.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.061][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.069][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.093][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:57.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:57.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.102][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:57.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:57.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:57.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:57.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:57.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:57.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.147][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:57.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.155][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 23:19:57.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.180][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:57.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.190][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.198][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.216][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:57.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:57.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:57.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:57.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:57.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:57.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:57.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:19:57.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:19:57.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:19:57.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.403][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:57.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:19:57.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.414][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:57.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:19:57.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.424][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:19:57.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:19:57.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.461][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:57.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:57.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.470][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:19:57.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:57.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:57.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:57.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.487][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:19:57.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:19:57.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.514][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.523][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 23:19:57.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:19:57.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.549][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:19:57.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:19:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.559][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.585][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:19:57.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:19:57.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:57.711][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-10-16 23:19:57.741][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 23:19:57.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:57.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:57.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:57.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:57.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:57.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:57.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:19:57.769][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.778][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.787][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:57.789][private$selectFields]
biodb.TRACE[2024-10-16 23:19:57.791][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:19:57.794][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:19:57.800][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:57.804][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.806][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.810][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.812][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.815][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.819][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.822][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:57.825][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:57.840][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.843][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.848][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.850][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:19:57.852][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.878][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.890][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:57.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:57.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:57.927][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-16 23:19:57.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:57.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:57.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:57.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:57.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:57.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:58.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:19:58.079][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.088][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.096][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.098][private$selectFields]
biodb.TRACE[2024-10-16 23:19:58.100][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:19:58.101][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:19:58.103][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.258][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.262][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.267][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.269][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.272][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.277][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.279][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.281][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.283][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.286][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.293][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:19:58.295][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.303][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.311][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.320][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-16 23:19:58.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:58.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:58.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:58.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:58.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:58.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:58.344][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:19:58.411][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.427][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.438][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.443][private$selectFields]
biodb.TRACE[2024-10-16 23:19:58.445][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:19:58.447][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:19:58.449][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.451][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.529][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.533][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.536][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.538][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.542][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.544][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.546][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:19:58.548][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.551][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.556][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.560][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:19:58.562][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.572][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.581][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:19:58.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.592][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-16 23:19:58.594][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 23:19:58.596][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 23:19:58.615][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 23:19:58.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 23:19:58.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 23:19:58.634][biodb::testThat]
biodb.INFO [2024-10-16 23:19:58.699][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-16 23:19:58.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:19:58.705][biodb::testThat]
biodb.TRACE[2024-10-16 23:19:58.715][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 23:19:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 23:19:58.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 23:19:58.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 23:19:58.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:19:58.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:19:58.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:19:58.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:19:59.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:19:59.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:19:59.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:19:59.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:19:59.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:19:59.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:19:59.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:19:59.143][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[2024-10-16 23:19:59.151][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:19:59.154][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5652f5994fce967a05a065a71bac3ed6".
biodb.TRACE[2024-10-16 23:19:59.157][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:19:59.638][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content".
biodb.DEBUG[2024-10-16 23:20:02.419][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 23:20:02.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:02.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:02.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:02.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:02.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:02.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:02.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:20:02.763][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.773][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.814][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.816][private$selectFields]
biodb.TRACE[2024-10-16 23:20:02.818][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:20:02.820][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:20:02.823][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.825][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.827][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.831][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.833][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.836][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.840][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.842][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.860][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.863][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.865][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.869][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.871][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:20:02.874][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.882][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.900][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-16 23:20:02.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:02.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:02.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:02.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:02.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:02.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:02.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:20:02.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.939][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.948][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.949][private$selectFields]
biodb.TRACE[2024-10-16 23:20:02.951][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:20:02.953][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:20:02.955][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.957][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.959][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.962][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.964][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.966][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.970][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.972][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.974][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:02.976][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.978][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.982][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.984][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:20:02.986][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:02.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:02.995][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:02.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.004][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.012][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-16 23:20:03.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:03.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:03.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:03.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:03.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:03.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:03.034][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:20:03.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.045][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.053][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:03.055][private$selectFields]
biodb.TRACE[2024-10-16 23:20:03.057][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:20:03.059][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:20:03.061][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:03.063][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.065][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.069][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.071][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.073][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.078][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:03.080][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:03.082][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.084][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.088][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.090][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:20:03.092][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.100][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.108][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:03.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.117][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-16 23:20:03.119][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 23:20:03.121][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 23:20:03.216][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 23:20:03.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 23:20:03.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 23:20:03.242][biodb::testThat]
biodb.INFO [2024-10-16 23:20:03.245][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-16 23:20:03.247][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:03.249][biodb::testThat]
biodb.TRACE[2024-10-16 23:20:03.256][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 23:20:03.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 23:20:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 23:20:03.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 23:20:03.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:03.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:03.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:03.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:20:03.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:03.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:03.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:03.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:03.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:03.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:03.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:03.422][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[2024-10-16 23:20:03.428][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:20:03.432][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-10-16 23:20:03.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:20:03.645][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-10-16 23:20:06.344][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 23:20:06.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:06.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:06.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:07.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:07.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:07.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:07.604][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:20:07.607][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.680][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.688][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:07.690][private$selectFields]
biodb.TRACE[2024-10-16 23:20:07.692][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:20:07.696][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:20:07.698][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:07.700][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.702][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.706][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.708][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.881][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.885][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.888][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:07.890][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:07.892][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.895][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.900][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.903][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:20:07.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.921][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:07.929][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-16 23:20:07.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:07.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:07.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:07.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:07.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:07.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:07.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:20:07.957][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:07.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:07.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.086][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.094][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.096][private$selectFields]
biodb.TRACE[2024-10-16 23:20:08.098][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:20:08.100][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:20:08.102][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.104][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.106][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.110][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.112][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.199][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.205][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.207][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.209][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.211][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.213][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.217][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.219][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:20:08.221][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.230][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.241][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.250][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-16 23:20:08.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:08.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:08.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:08.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:08.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:08.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:08.273][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:20:08.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.284][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.294][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.295][private$selectFields]
biodb.TRACE[2024-10-16 23:20:08.298][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 23:20:08.300][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:20:08.302][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.304][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.306][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.312][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.314][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.318][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.320][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.322][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:20:08.324][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.326][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.331][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.333][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 23:20:08.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.343][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:08.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:08.360][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-16 23:20:08.362][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 23:20:08.364][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 23:20:08.507][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 23:20:08.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 23:20:08.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:08.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 23:20:08.626][biodb::testThat]
biodb.INFO [2024-10-16 23:20:08.628][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-16 23:20:08.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:08.632][biodb::testThat]
biodb.DEBUG[2024-10-16 23:20:08.636][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-16 23:20:08.638][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 23:20:08.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-16 23:20:08.644][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 23:20:08.646][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 23:20:08.649][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 23:20:08.816][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 23:20:08.819][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 23:20:08.821][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 23:20:08.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:08.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:08.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:08.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:08.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:08.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:08.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:08.851][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-10-16 23:20:08.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:08.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 23:20:08.861][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:09.083][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:09.085][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:09.087][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[2024-10-16 23:20:09.090][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:09.400][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:09.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:09.404][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:09.532][rule$waitAsNeeded] Wait 0.328543 second(s).
biodb.TRACE[2024-10-16 23:20:10.129][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:10.350][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:10.353][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:10.355][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:10.357][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:10.667][private$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[2024-10-16 23:20:10.670][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:10.672][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:10.675][rule$waitAsNeeded] Wait 0.454283 second(s).
biodb.TRACE[2024-10-16 23:20:11.138][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:11.365][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:11.368][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:11.370][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[2024-10-16 23:20:11.373][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:11.677][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:11.679][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:11.681][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:11.684][rule$waitAsNeeded] Wait 0.453889 second(s).
biodb.TRACE[2024-10-16 23:20:12.157][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:12.390][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:12.392][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:12.394][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:12.397][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:12.705][private$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[2024-10-16 23:20:12.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:12.708][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:12.709][rule$waitAsNeeded] Wait 0.446678 second(s).
biodb.TRACE[2024-10-16 23:20:13.173][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:13.382][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:13.384][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:13.385][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[2024-10-16 23:20:13.387][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:13.681][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:13.683][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:13.684][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:13.685][rule$waitAsNeeded] Wait 0.487064 second(s).
biodb.TRACE[2024-10-16 23:20:14.190][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:14.411][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:14.413][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:14.415][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:14.417][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:14.723][private$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[2024-10-16 23:20:14.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:14.728][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:14.730][rule$waitAsNeeded] Wait 0.459136 second(s).
biodb.TRACE[2024-10-16 23:20:15.206][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:15.437][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:15.439][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:15.441][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[2024-10-16 23:20:15.443][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:15.752][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:15.754][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:15.756][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:15.759][rule$waitAsNeeded] Wait 0.446356 second(s).
biodb.TRACE[2024-10-16 23:20:16.222][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:16.446][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:16.448][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:16.452][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:16.454][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:16.798][private$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[2024-10-16 23:20:16.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:16.802][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:16.804][rule$waitAsNeeded] Wait 0.417323 second(s).
biodb.TRACE[2024-10-16 23:20:17.238][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:17.454][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:17.456][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:17.458][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[2024-10-16 23:20:17.460][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:17.780][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:17.782][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:17.784][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:17.787][rule$waitAsNeeded] Wait 0.450794 second(s).
biodb.TRACE[2024-10-16 23:20:18.254][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 23:20:18.483][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:18.485][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:18.487][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:18.490][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 23:20:18.798][private$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[2024-10-16 23:20:18.803][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-10-16 23:20:18.808][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 23:20:18.811][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-16 23:20:18.813][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 23:20:18.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:18.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:18.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:19.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:19.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:19.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:19.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:20:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:19.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:19.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:19.527][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:19.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:19.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:19.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:19.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:19.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:19.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:19.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:19.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:19.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:19.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:19.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:19.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:19.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:19.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:19.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:19.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:19.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:19.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:19.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:19.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:20:19.725][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-10-16 23:20:19.727][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-16 23:20:19.748][biodb::testThat]
biodb.INFO [2024-10-16 23:20:19.916][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-16 23:20:19.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:19.920][biodb::testThat]
biodb.DEBUG[2024-10-16 23:20:19.942][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-10-16 23:20:19.944][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-10-16 23:20:19.946][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-16 23:20:19.949][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-10-16 23:20:19.953][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2024-10-16 23:20:19.969][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2024-10-16 23:20:20.061][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 23:20:20.064][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 23:20:20.067][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 23:20:20.069][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 23:20:20.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:20.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:20.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:20.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:20.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:20.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:20.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:20.212][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-10-16 23:20:20.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:20.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 23:20:20.242][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:20.457][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:20.459][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:20.461][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[2024-10-16 23:20:20.464][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:20.798][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:20.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:20.802][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:20.805][rule$waitAsNeeded] Wait 0.437113 second(s).
biodb.TRACE[2024-10-16 23:20:21.256][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:21.481][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:21.483][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:21.485][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:21.488][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:21.795][private$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[2024-10-16 23:20:21.798][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:21.801][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:21.803][rule$waitAsNeeded] Wait 0.451707 second(s).
biodb.TRACE[2024-10-16 23:20:22.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:22.569][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:22.571][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:22.573][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[2024-10-16 23:20:22.575][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:23.103][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:23.106][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:23.108][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:23.110][rule$waitAsNeeded] Wait 0.242214 second(s).
biodb.TRACE[2024-10-16 23:20:23.366][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:27.023][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:27.025][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:27.026][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:27.027][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:27.327][private$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[2024-10-16 23:20:27.328][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:27.329][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 23:20:27.331][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:27.529][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:27.530][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:27.532][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:27.533][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:27.830][private$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[2024-10-16 23:20:27.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:27.833][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:27.834][rule$waitAsNeeded] Wait 0.496252 second(s).
biodb.TRACE[2024-10-16 23:20:28.336][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:28.539][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:28.540][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:28.542][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[2024-10-16 23:20:28.543][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:28.845][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:28.846][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:28.847][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:28.848][rule$waitAsNeeded] Wait 0.487362 second(s).
biodb.TRACE[2024-10-16 23:20:29.352][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:29.570][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:29.572][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:29.574][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:29.576][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:29.881][private$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[2024-10-16 23:20:29.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:29.885][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:29.887][rule$waitAsNeeded] Wait 0.46504 second(s).
biodb.TRACE[2024-10-16 23:20:30.386][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:30.621][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:30.623][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:30.626][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[2024-10-16 23:20:30.628][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:31.148][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 23:20:31.151][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:31.153][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:31.155][rule$waitAsNeeded] Wait 0.230897 second(s).
biodb.TRACE[2024-10-16 23:20:31.401][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:34.099][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:34.101][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:34.103][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:34.105][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:34.401][private$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[2024-10-16 23:20:34.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:34.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 23:20:34.406][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 23:20:34.612][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 23:20:34.613][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:34.615][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:34.616][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 23:20:34.914][private$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[2024-10-16 23:20:34.927][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv"
biodb.DEBUG[2024-10-16 23:20:34.931][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 23:20:34.933][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-16 23:20:34.935][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 23:20:34.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:34.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:34.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:40.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:40.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:40.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:40.351][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:20:40.353][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.358][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:20:40.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:20:40.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:40.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:40.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:40.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:40.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:40.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:20:40.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:20:40.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:20:40.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:20:40.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:20:40.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.420][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:20:40.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:20:40.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.424][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:20:40.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:20:40.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.429][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:20:40.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:20:40.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.434][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:20:40.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:20:40.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.439][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:20:40.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:20:40.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.444][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:20:40.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:20:40.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:20:40.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:20:40.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:20:40.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:20:40.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.461][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:20:40.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:40.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.466][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:20:40.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:40.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:20:40.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:20:40.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:20:40.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:20:40.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.490][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:20:40.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.494][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 23:20:40.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.508][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:20:40.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:40.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:40.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.536][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.540][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:20:40.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:40.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:20:40.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:20:40.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:40.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:20:40.604][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2024-10-16 23:20:40.605][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-16 23:20:40.606][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-16 23:20:40.723][biodb::testThat]
biodb.INFO [2024-10-16 23:20:40.725][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-16 23:20:40.726][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:40.727][biodb::testThat]
biodb.INFO [2024-10-16 23:20:41.352][biodb::testThat]
biodb.INFO [2024-10-16 23:20:41.354][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-16 23:20:41.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:41.356][biodb::testThat]
biodb.INFO [2024-10-16 23:20:41.369][biodb::testThat]
biodb.INFO [2024-10-16 23:20:41.370][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-16 23:20:41.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:41.373][biodb::testThat]
biodb.DEBUG[2024-10-16 23:20:41.376][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[2024-10-16 23:20:41.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:20:41.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-10-16 23:20:41.383][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:20:41.839][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2024-10-16 23:20:47.817][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:20:47.818][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:20:47.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:47.821][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:20:47.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:47.823][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:20:47.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:20:47.827][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 23:20:47.829][biodb::testThat]
biodb.INFO [2024-10-16 23:20:47.830][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-16 23:20:47.832][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:47.833][biodb::testThat]
biodb.ERROR[2024-10-16 23:20:48.042][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-16 23:20:50.765][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-16 23:20:50.780][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 23:20:50.781][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-16 23:20:50.783][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-16 23:20:50.784][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 23:20:50.785][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:50.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:50.787][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:50.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:50.789][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:50.790][FUN] Functions in observer BiodbConfig: [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 [2024-10-16 23:20:51.279][biodb::testContext]
biodb.INFO [2024-10-16 23:20:51.280][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 23:20:51.282][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-10-16 23:20:51.283][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 23:20:51.284][biodb::testContext]
biodb.INFO [2024-10-16 23:20:51.308][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 23:20:51.312][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 23:20:52.331][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:20:52.332][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 23:20:52.334][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 23:20:52.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.339][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 23:20:52.341][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 23:20:52.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.345][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 23:20:52.347][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 23:20:52.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.351][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 23:20:52.352][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 23:20:52.353][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 23:20:52.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.358][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 23:20:52.359][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 23:20:52.360][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 23:20:52.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.364][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 23:20:52.365][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 23:20:52.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.370][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 23:20:52.371][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 23:20:52.372][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 23:20:52.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.376][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 23:20:52.378][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 23:20:52.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.382][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 23:20:52.383][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 23:20:52.384][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 23:20:52.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.388][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 23:20:52.390][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 23:20:52.391][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 23:20:52.392][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 23:20:52.393][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 23:20:52.394][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 23:20:52.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.399][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 23:20:52.400][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 23:20:52.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.404][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 23:20:52.405][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 23:20:52.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.410][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 23:20:52.411][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 23:20:52.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.415][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 23:20:52.416][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 23:20:52.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.421][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 23:20:52.422][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 23:20:52.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.426][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 23:20:52.427][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 23:20:52.430][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 23:20:52.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.434][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[2024-10-16 23:20:52.435][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 23:20:52.436][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 23:20:52.437][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 23:20:52.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.442][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 23:20:52.465][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.467][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 23:20:52.468][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.469][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:20:52.470][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.472][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.473][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.475][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:20:52.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:20:52.477][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.479][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 23:20:52.480][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:20:52.481][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:20:52.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:20:52.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 23:20:52.483][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 23:20:52.483][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 23:20:52.485][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:20:52.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.488][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:20:52.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.492][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:20:52.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:20:52.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.497][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.498][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 23:20:52.501][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.502][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 23:20:52.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:20:52.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.507][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.508][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.509][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.510][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 23:20:52.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:20:52.512][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.514][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 23:20:52.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:20:52.516][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.517][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.518][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:20:52.518][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:20:52.518][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 23:20:52.518][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 23:20:52.518][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 23:20:52.519][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:20:52.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.523][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:20:52.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.526][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.527][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.529][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:20:52.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:20:52.531][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.532][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.533][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 23:20:52.535][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.536][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 23:20:52.538][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.539][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:20:52.540][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.542][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.544][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.545][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:20:52.546][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:20:52.547][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.548][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 23:20:52.550][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:20:52.551][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.552][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.553][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.554][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:20:52.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.558][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:20:52.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.561][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.562][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.564][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:20:52.565][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:20:52.578][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.579][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.581][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 23:20:52.582][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.584][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 23:20:52.585][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:20:52.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.588][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.591][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.592][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 23:20:52.593][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:20:52.594][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.595][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 23:20:52.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:20:52.598][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.599][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:52.600][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.601][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:20:52.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.604][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:20:52.606][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:52.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:52.608][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:20:52.609][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:20:52.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:20:52.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:52.613][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:52.615][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:20:52.616][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.680][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[2024-10-16 23:20:52.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.707][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 23:20:52.708][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 23:20:52.710][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 23:20:52.712][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 23:20:52.713][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 23:20:52.715][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 23:20:52.716][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 23:20:52.718][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 23:20:52.719][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 23:20:52.721][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 23:20:52.722][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 23:20:52.724][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 23:20:52.725][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 23:20:52.727][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 23:20:52.728][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 23:20:52.730][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 23:20:52.731][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 23:20:52.733][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 23:20:52.734][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 23:20:52.736][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 23:20:52.737][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 23:20:52.739][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 23:20:52.740][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 23:20:52.742][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 23:20:52.744][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 23:20:52.745][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 23:20:52.747][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 23:20:52.748][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 23:20:52.750][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 23:20:52.751][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 23:20:52.753][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 23:20:52.754][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 23:20:52.756][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 23:20:52.757][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 23:20:52.759][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 23:20:52.760][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 23:20:52.762][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 23:20:52.763][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 23:20:52.765][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 23:20:52.766][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 23:20:52.768][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 23:20:52.769][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 23:20:52.771][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 23:20:52.772][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 23:20:52.774][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 23:20:52.776][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 23:20:52.777][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 23:20:52.779][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 23:20:52.780][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 23:20:52.782][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 23:20:52.783][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 23:20:52.785][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 23:20:52.786][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 23:20:52.788][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 23:20:52.789][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 23:20:52.791][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 23:20:52.792][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 23:20:52.794][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 23:20:52.796][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 23:20:52.797][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 23:20:52.799][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 23:20:52.800][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 23:20:52.802][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 23:20:52.804][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 23:20:52.805][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 23:20:52.807][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 23:20:52.808][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 23:20:52.810][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 23:20:52.811][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 23:20:52.813][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 23:20:52.814][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 23:20:52.816][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 23:20:52.817][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 23:20:52.819][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 23:20:52.820][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 23:20:52.822][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 23:20:52.823][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 23:20:52.825][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 23:20:52.826][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 23:20:52.828][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 23:20:52.829][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 23:20:52.831][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 23:20:52.832][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 23:20:52.834][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 23:20:52.836][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 23:20:52.838][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:20:52.839][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.841][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.842][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[2024-10-16 23:20:52.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.864][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[2024-10-16 23:20:52.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.871][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[2024-10-16 23:20:52.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.893][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[2024-10-16 23:20:52.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.908][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[2024-10-16 23:20:52.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.928][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[2024-10-16 23:20:52.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.957][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[2024-10-16 23:20:52.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:52.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:20:52.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:20:52.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:20:52.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:20:52.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:20:52.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:20:52.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:20:53.142][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-16 23:20:53.297][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:20:53.300][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:53.302][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 23:20:53.304][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:53.305][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:20:53.307][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:53.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:20:53.309][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:53.310][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:20:53.311][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:20:53.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:20:53.314][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:53.315][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-16 23:20:53.316][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-16 23:20:53.317][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-16 23:20:53.319][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 23:20:53.320][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:20:53.320][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:20:53.321][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:20:53.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:53.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:53.324][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:20:53.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:20:53.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:20:53.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:20:53.329][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 23:20:53.329][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-16 23:20:53.330][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:20:53.331][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:20:53.332][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 23:20:53.333][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:20:53.335][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-16 23:20:53.336][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 23:20:53.340][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:20:53.341][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-16 23:20:53.342][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:20:53.344][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-16 23:20:53.345][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 23:20:53.346][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 23:20:53.348][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-16 23:20:53.349][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-16 23:20:53.351][biodb::testThat]
biodb.INFO [2024-10-16 23:20:53.352][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-10-16 23:20:53.353][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:53.355][biodb::testThat]
biodb.DEBUG[2024-10-16 23:20:53.358][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[2024-10-16 23:20:53.364][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:53.365][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 23:20:53.367][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-10-16 23:20:53.566][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride does not exist.
biodb.TRACE[2024-10-16 23:20:53.568][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:53.570][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:53.571][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-10-16 23:20:53.916][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 23:20:53.919][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-10-16 23:20:53.924][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-10-16 23:20:54.668][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-10-16 23:20:54.673][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:20:54.676][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2024-10-16 23:20:54.679][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:20:54.724][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2024-10-16 23:20:54.754][biodb::testThat]
biodb.INFO [2024-10-16 23:20:54.756][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-10-16 23:20:54.758][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:54.760][biodb::testThat]
biodb.INFO [2024-10-16 23:20:54.793][biodb::testThat]
biodb.INFO [2024-10-16 23:20:54.794][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-10-16 23:20:54.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:20:54.797][biodb::testThat]
biodb.DEBUG[2024-10-16 23:20:54.800][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-16 23:20:54.804][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:54.805][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 23:20:54.807][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-10-16 23:20:55.013][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-10-16 23:20:55.014][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:55.016][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:55.018][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-10-16 23:20:55.311][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 23:20:55.314][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-10-16 23:20:55.319][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-10-16 23:20:55.325][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[2024-10-16 23:20:55.328][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:20:55.330][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-10-16 23:20:55.332][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:20:55.341][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-10-16 23:20:55.347][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[2024-10-16 23:20:55.351][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:55.352][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:55.353][rule$waitAsNeeded] Wait 0.452985 second(s).
biodb.TRACE[2024-10-16 23:20:55.812][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-10-16 23:20:56.014][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-10-16 23:20:56.015][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:56.017][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:56.019][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-10-16 23:20:56.311][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 23:20:56.313][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-10-16 23:20:56.319][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-10-16 23:20:56.327][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[2024-10-16 23:20:56.330][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:56.331][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 23:20:56.333][rule$waitAsNeeded] Wait 0.478056 second(s).
biodb.TRACE[2024-10-16 23:20:56.828][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-10-16 23:20:57.033][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2024-10-16 23:20:57.034][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:57.036][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:57.037][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-10-16 23:20:58.314][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 23:20:58.317][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-10-16 23:20:58.333][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-10-16 23:20:58.524][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[2024-10-16 23:20:58.528][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 23:20:58.529][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 23:20:58.532][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-10-16 23:20:58.731][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6 does not exist.
biodb.TRACE[2024-10-16 23:20:58.732][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 23:20:58.734][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 23:20:58.736][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-10-16 23:20:59.830][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 23:20:59.833][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-10-16 23:20:59.851][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-10-16 23:21:00.133][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 23:21:00.135][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-16 23:21:00.137][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-16 23:21:00.139][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 23:21:00.141][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:00.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:00.144][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:00.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:00.148][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:00.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 23:21:00.293][biodb::testContext]
biodb.INFO [2024-10-16 23:21:00.294][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 23:21:00.296][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-10-16 23:21:00.297][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 23:21:00.298][biodb::testContext]
biodb.INFO [2024-10-16 23:21:00.339][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 23:21:00.345][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 23:21:01.693][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:21:01.695][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 23:21:01.697][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 23:21:01.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.701][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 23:21:01.703][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 23:21:01.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.707][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 23:21:01.708][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 23:21:01.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.714][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 23:21:01.716][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 23:21:01.718][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 23:21:01.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.723][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 23:21:01.724][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 23:21:01.725][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 23:21:01.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.731][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 23:21:01.732][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 23:21:01.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.737][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 23:21:01.738][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 23:21:01.739][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 23:21:01.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.743][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 23:21:01.745][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 23:21:01.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.749][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 23:21:01.750][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 23:21:01.751][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 23:21:01.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.756][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 23:21:01.757][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 23:21:01.758][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 23:21:01.759][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 23:21:01.760][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 23:21:01.762][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 23:21:01.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.766][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 23:21:01.767][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 23:21:01.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.771][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 23:21:01.773][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 23:21:01.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.777][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 23:21:01.778][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 23:21:01.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.781][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[2024-10-16 23:21:01.782][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 23:21:01.784][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 23:21:01.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.788][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 23:21:01.789][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 23:21:01.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.792][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[2024-10-16 23:21:01.794][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 23:21:01.795][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 23:21:01.798][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 23:21:01.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.803][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 23:21:01.804][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 23:21:01.805][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 23:21:01.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.810][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 23:21:01.812][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.813][self$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[2024-10-16 23:21:01.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.815][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:21:01.817][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.818][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.819][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.820][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.821][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:21:01.823][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:21:01.824][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.825][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 23:21:01.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:21:01.827][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.829][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.830][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:21:01.830][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:21:01.830][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 23:21:01.830][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 23:21:01.830][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 23:21:01.831][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:21:01.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:21:01.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.838][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.839][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:21:01.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:21:01.842][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.844][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.845][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 23:21:01.847][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.848][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 23:21:01.849][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.851][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:21:01.852][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.853][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.854][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.855][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.857][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 23:21:01.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:21:01.859][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.860][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 23:21:01.862][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:21:01.863][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.864][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.865][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:21:01.865][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:21:01.865][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 23:21:01.865][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 23:21:01.865][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 23:21:01.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:21:01.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.870][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:21:01.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.875][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:21:01.877][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:21:01.878][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.880][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.881][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 23:21:01.883][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.884][self$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[2024-10-16 23:21:01.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.887][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:21:01.888][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.889][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.890][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.892][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.893][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:21:01.894][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:21:01.895][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.897][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 23:21:01.898][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:21:01.899][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.900][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.901][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.903][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:21:01.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.906][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:21:01.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.912][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.914][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:21:01.917][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:21:01.919][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.921][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.923][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 23:21:01.926][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.928][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 23:21:01.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.932][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:21:01.933][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.937][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.939][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.941][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 23:21:01.943][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:21:01.945][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.947][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 23:21:01.948][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:21:01.950][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.952][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:01.954][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:21:01.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.961][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:21:01.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:01.965][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:01.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:21:01.968][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.970][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:21:01.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:21:01.974][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:01.976][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:01.978][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:21:01.980][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.982][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[2024-10-16 23:21:01.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:01.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:01.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:01.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:01.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:01.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:01.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:01.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.017][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[2024-10-16 23:21:02.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.107][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 23:21:02.121][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 23:21:02.122][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 23:21:02.124][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 23:21:02.125][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 23:21:02.127][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 23:21:02.128][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 23:21:02.130][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 23:21:02.132][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 23:21:02.133][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 23:21:02.135][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 23:21:02.136][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 23:21:02.138][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 23:21:02.139][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 23:21:02.141][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 23:21:02.142][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 23:21:02.144][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 23:21:02.147][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 23:21:02.149][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 23:21:02.153][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 23:21:02.155][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 23:21:02.158][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 23:21:02.161][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 23:21:02.165][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 23:21:02.168][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 23:21:02.171][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 23:21:02.184][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 23:21:02.187][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 23:21:02.190][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 23:21:02.195][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 23:21:02.199][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 23:21:02.201][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 23:21:02.203][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 23:21:02.205][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 23:21:02.207][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 23:21:02.209][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 23:21:02.210][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 23:21:02.212][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 23:21:02.213][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 23:21:02.215][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 23:21:02.217][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 23:21:02.218][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 23:21:02.220][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 23:21:02.221][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 23:21:02.223][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 23:21:02.224][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 23:21:02.226][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 23:21:02.227][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 23:21:02.229][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 23:21:02.230][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 23:21:02.232][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 23:21:02.233][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 23:21:02.235][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 23:21:02.237][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 23:21:02.238][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 23:21:02.240][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 23:21:02.241][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 23:21:02.243][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 23:21:02.244][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 23:21:02.246][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 23:21:02.247][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 23:21:02.249][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 23:21:02.251][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 23:21:02.252][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 23:21:02.254][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 23:21:02.255][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 23:21:02.257][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 23:21:02.258][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 23:21:02.260][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 23:21:02.261][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 23:21:02.263][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 23:21:02.265][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 23:21:02.266][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 23:21:02.268][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 23:21:02.269][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 23:21:02.271][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 23:21:02.272][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 23:21:02.274][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 23:21:02.275][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 23:21:02.277][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 23:21:02.278][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 23:21:02.280][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 23:21:02.282][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 23:21:02.283][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 23:21:02.286][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 23:21:02.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 23:21:02.288][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.290][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.336][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[2024-10-16 23:21:02.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.358][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[2024-10-16 23:21:02.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:02.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 23:21:02.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:02.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:02.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:02.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:02.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:02.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 23:21:03.303][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-16 23:21:03.313][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:21:03.315][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:03.316][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 23:21:03.317][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:03.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 23:21:03.320][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:03.321][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 23:21:03.322][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:03.323][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 23:21:03.324][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 23:21:03.326][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 23:21:03.327][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:03.328][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-16 23:21:03.329][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-16 23:21:03.330][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-16 23:21:03.332][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 23:21:03.333][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 23:21:03.333][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 23:21:03.334][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 23:21:03.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:03.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:03.337][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 23:21:03.339][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 23:21:03.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 23:21:03.341][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 23:21:03.342][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 23:21:03.342][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-16 23:21:03.343][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 23:21:03.344][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 23:21:03.345][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 23:21:03.347][self$setPropertyValue]
biodb.DEBUG[2024-10-16 23:21:03.348][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-16 23:21:03.350][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 23:21:03.353][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:21:03.354][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-16 23:21:03.355][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 23:21:03.357][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-16 23:21:03.358][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 23:21:03.360][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 23:21:03.361][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-16 23:21:03.362][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-16 23:21:03.365][biodb::testThat]
biodb.INFO [2024-10-16 23:21:03.366][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-10-16 23:21:03.367][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 23:21:03.368][biodb::testThat]
biodb.DEBUG[2024-10-16 23:21:03.372][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-16 23:21:03.377][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 23:21:03.379][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-10-16 23:21:03.380][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 23:21:03.513][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-10-16 23:21:05.276][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-10-16 23:21:05.278][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-16 23:21:05.281][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-10-16 23:21:05.284][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-10-16 23:21:05.290][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-10-16 23:21:05.292][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 23:21:05.294][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-16 23:21:05.297][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 23:21:05.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:21:05.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:05.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:06.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:06.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:06.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:06.209][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:21:06.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:06.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:06.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:06.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:06.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:06.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:06.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:06.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:06.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.235][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:21:06.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:21:06.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.240][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:21:06.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:21:06.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.245][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:06.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:06.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.250][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:06.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:06.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:06.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:06.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.260][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:06.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:06.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.265][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:21:06.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:06.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.270][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:21:06.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:06.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:06.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:06.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:06.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:06.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.297][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:21:06.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.302][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 23:21:06.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.324][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:21:06.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:06.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:06.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.356][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:06.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:06.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.361][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:06.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:06.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:06.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:06.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:06.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:06.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:06.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:06.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:06.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:06.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:06.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:06.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:06.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:06.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:21:06.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:21:06.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:06.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:08.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:08.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:08.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:08.015][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:21:08.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.038][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:21:08.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 23:21:08.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.043][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:21:08.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 23:21:08.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.048][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.053][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.062][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.067][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:21:08.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.072][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 23:21:08.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.077][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.096][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:21:08.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.101][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 23:21:08.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.116][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 23:21:08.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.121][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.125][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.135][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 23:21:08.195][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-10-16 23:21:08.198][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 23:21:08.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:21:08.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:08.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:08.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:08.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:08.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:08.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 23:21:08.489][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:21:08.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:21:08.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:21:08.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:21:08.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 23:21:08.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 23:21:08.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.503][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 23:21:08.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 23:21:08.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.508][private$selectFields] Fields none
biodb.TRACE[2024-10-16 23:21:08.509][private$selectFields]
biodb.TRACE[2024-10-16 23:21:08.510][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-16 23:21:08.511][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:21:08.512][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:21:08.513][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.515][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.517][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.518][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.524][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.526][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.528][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.532][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.533][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.535][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.539][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.541][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.543][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.547][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.548][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.550][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.554][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.556][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.558][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.561][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.563][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.565][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.569][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.571][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.573][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.577][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.578][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.581][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.584][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.586][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.588][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.592][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.593][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.595][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.599][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.607][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.609][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.611][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.615][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.617][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.623][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.625][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.627][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.631][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.633][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:21:08.635][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:21:08.637][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.639][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.643][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.645][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.647][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.650][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.652][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.655][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.658][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.660][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.663][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.666][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.668][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.670][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.674][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.676][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.678][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.682][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.684][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.686][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.690][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.692][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.694][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.698][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.700][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-10-16 23:21:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:08.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:08.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:08.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.749][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.757][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:08.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.773][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.780][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:08.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:08.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.812][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.817][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:08.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:08.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:08.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:08.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.845][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.850][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:08.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:08.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:08.860][private$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[2024-10-16 23:21:08.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 23:21:08.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:08.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:09.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:09.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:09.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:09.648][FUN] Functions in observer BiodbConfig: [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[2024-10-16 23:21:09.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:21:09.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:21:09.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.655][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 23:21:09.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 23:21:09.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 23:21:09.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 23:21:09.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 23:21:09.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 23:21:09.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.670][private$selectFields] Fields none
biodb.TRACE[2024-10-16 23:21:09.672][private$selectFields]
biodb.TRACE[2024-10-16 23:21:09.673][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-16 23:21:09.674][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 23:21:09.675][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:21:09.677][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:09.679][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:09.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.683][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.687][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.690][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.692][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.694][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.698][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.700][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.723][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.727][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.729][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.731][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.735][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.737][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:09.739][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:09.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.742][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.743][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:09.744][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:09.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.746][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.748][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.749][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.751][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.752][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:09.754][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:09.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.756][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.757][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.758][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.760][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.762][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.763][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.765][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.766][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.767][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.770][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.771][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.772][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.774][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.775][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:09.777][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:09.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.779][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.780][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:09.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:09.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.783][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.785][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.786][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.788][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.789][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:21:09.790][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 23:21:09.792][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:09.793][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:09.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.795][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.796][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.800][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.801][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.802][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.804][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.806][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.807][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.809][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.810][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.814][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.815][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:09.816][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:09.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.818][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.820][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:09.821][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:09.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.823][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.824][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.825][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.828][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.829][private$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[2024-10-16 23:21:09.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:09.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:09.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:09.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:09.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 23:21:09.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 23:21:09.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 23:21:09.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.858][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.868][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 23:21:09.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.878][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 23:21:09.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 23:21:09.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:09.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:09.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:09.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:09.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.911][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 23:21:09.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 23:21:09.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:09.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:09.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:09.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:09.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 23:21:09.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 23:21:09.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.930][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.934][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.939][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 23:21:09.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 23:21:09.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 23:21:09.947][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-10-16 23:21:09.948][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 23:21:09.950][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-10-16 23:21:11.460][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 23:21:11.463][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-16 23:21:11.465][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-16 23:21:11.467][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 23:21:11.469][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 23:21:11.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 23:21:11.473][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 23:21:11.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 23:21:11.476][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 23:21:11.478][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 165 ]
> 
> proc.time()
   user  system elapsed 
  26.04    1.50   90.20

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn 3.51 1.7446.57
LipidmapsStructureEntry0.700.030.74