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This page was generated on 2024-10-18 20:40 -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 merida1

To the developers/maintainers of the biodbLipidmaps package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-10-17 01:50:12 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 01:55:11 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 299.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 5.045  1.933  21.733
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 [2024-10-17 01:52:50.674][biodb::testContext]
biodb.INFO [2024-10-17 01:52:50.692][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:50.696][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-17 01:52:50.702][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:50.718][biodb::testContext]
biodb.INFO [2024-10-17 01:52:50.758][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:50.762][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:50.796][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:50.799][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:52:50.816][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:52:50.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:50.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:50.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:50.842][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:52:51.057][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:52:51.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.073][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:52:51.077][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:52:51.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.090][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:52:51.108][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:52:51.115][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:52:51.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.133][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:52:51.137][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:52:51.139][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:52:51.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.160][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:52:51.163][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:52:51.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.184][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:52:51.187][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:52:51.203][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:52:51.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.225][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:52:51.227][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:52:51.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.234][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:52:51.239][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:52:51.242][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:52:51.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.256][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:51.258][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:52:51.260][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:52:51.262][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:52:51.265][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:52:51.268][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:52:51.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.277][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:52:51.279][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:52:51.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.290][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:52:51.293][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:52:51.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.303][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:52:51.306][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:52:51.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.326][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:52:51.328][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:52:51.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.336][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:52:51.339][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:52:51.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.345][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:51.346][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:52:51.475][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:52:51.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.483][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:52:51.486][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:52:51.488][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:52:51.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:51.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:51.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:51.503][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:52:51.711][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:51.827][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 01:52:51.839][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:51.841][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:51.843][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:51.846][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:51.863][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:51.866][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:51.868][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:51.871][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:51.884][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:51.888][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:52:51.891][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:51.894][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:51.916][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:51.918][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:51.918][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:51.918][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:51.918][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:51.918][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:51.921][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:51.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:51.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:51.943][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:51.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:51.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:51.965][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:51.967][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:51.970][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:51.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:51.986][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:51.989][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:51.992][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:52:52.014][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.017][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:52.020][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.022][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:52.039][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.042][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.044][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.061][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:52.064][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:52.066][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.070][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:52:52.089][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:52.091][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.094][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.096][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:52.096][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:52.096][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:52.096][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:52.096][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:52.111][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:52.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:52.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:52.130][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:52.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:52.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:52.164][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.166][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.178][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:52.180][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:52.183][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.186][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.208][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:52:52.213][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.216][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 01:52:52.229][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.231][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:52.234][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.236][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.238][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.253][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.255][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:52.258][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:52.260][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.273][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:52:52.275][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:52.278][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.280][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.295][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.298][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:52.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:52.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:52.308][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:52.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:52.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:52.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.318][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.320][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:52.322][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:52.325][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.327][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.333][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:52:52.339][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.342][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:52.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.347][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:52.354][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.359][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.363][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.368][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:52.371][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:52.374][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.376][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:52:52.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:52.389][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.391][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:52.394][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.423][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:52.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:52.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:52.430][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:52.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:52.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:52.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:52.450][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.459][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:52.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:52.464][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:52.466][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:52.483][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:52.486][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.669][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[2024-10-17 01:52:52.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.690][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[2024-10-17 01:52:52.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.748][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[2024-10-17 01:52:52.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.792][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[2024-10-17 01:52:52.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:52.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:52.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:52.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:52.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:52.861][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:52:52.882][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:52:52.896][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:52:52.900][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:52:52.903][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:52:52.919][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:52:52.922][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:52.925][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:52.945][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:52:52.949][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:52:52.952][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:52:52.972][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:52:52.976][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:52.991][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:52.995][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:52:52.998][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:52:53.021][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:52:53.024][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:52:53.028][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:52:53.051][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:52:53.054][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:52:53.058][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:52:53.081][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:52:53.084][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:52:53.088][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:52:53.110][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:52:53.132][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:52:53.136][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:52:53.156][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:52:53.160][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:52:53.163][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:52:53.184][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:52:53.191][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:52:53.204][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:52:53.208][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:52:53.211][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:52:53.227][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:52:53.230][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:52:53.236][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:52:53.254][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:52:53.257][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:52:53.261][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:52:53.278][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:52:53.282][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:52:53.301][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:52:53.304][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:52:53.311][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:52:53.326][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:52:53.330][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:52:53.334][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:52:53.348][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:52:53.353][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:52:53.369][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:52:53.374][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:52:53.379][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:52:53.396][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:52:53.400][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:52:53.404][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:52:53.424][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:52:53.428][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:52:53.444][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:52:53.448][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:52:53.452][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:52:53.466][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:52:53.469][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:52:53.486][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:52:53.490][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:52:53.494][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:52:53.519][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:52:53.523][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:52:53.540][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:52:53.544][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:52:53.548][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:52:53.564][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:52:53.570][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:52:53.584][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:52:53.587][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:52:53.591][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:52:53.604][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:52:53.608][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:52:53.611][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:52:53.630][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:52:53.648][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:52:53.684][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:52:53.691][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:53.712][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:53.715][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:53.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:53.730][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:53.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:53.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:53.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:53.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:53.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:53.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:53.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:53.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:53.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:53.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:53.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:53.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:53.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:53.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:53.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:53.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:53.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:53.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:53.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:53.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:53.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:53.874][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[2024-10-17 01:52:53.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:53.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:53.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:53.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:53.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:53.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:53.908][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[2024-10-17 01:52:53.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:53.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:53.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:53.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:53.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:53.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:53.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:53.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:53.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:53.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:53.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:53.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:53.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:53.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.105][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[2024-10-17 01:52:54.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:54.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:54.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:54.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:54.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:54.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:54.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:54.417][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[2024-10-17 01:52:54.471][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:54.529][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:52:54.533][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:54.535][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:52:54.538][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:54.541][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:54.543][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:54.545][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:54.549][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:54.551][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:54.554][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:54.556][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:54.589][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:54.591][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-17 01:52:54.593][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-17 01:52:54.595][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-17 01:52:54.617][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:54.620][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:54.620][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:54.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:54.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:54.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:54.639][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:54.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:54.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:54.646][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:54.648][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 01:52:54.648][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-17 01:52:54.651][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:54.653][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:54.655][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:54.657][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:54.682][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-17 01:52:54.686][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:52:54.811][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:52:54.813][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-17 01:52:54.834][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:52:54.851][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-17 01:52:54.873][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 01:52:54.877][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 01:52:54.880][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-17 01:52:54.891][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-17 01:52:54.977][biodb::testThat]
biodb.INFO [2024-10-17 01:52:54.980][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-17 01:52:54.992][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:54.995][biodb::testThat]
biodb.TRACE[2024-10-17 01:52:55.023][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-10-17 01:52:55.027][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:52:55.046][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 01:52:55.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:55.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:55.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:55.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:55.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:55.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:55.210][FUN] Functions in observer BiodbConfig: [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[2024-10-17 01:52:55.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:55.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:55.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:55.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:55.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:55.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:55.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.412][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:52:55.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:52:55.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.437][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:55.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.478][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:55.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:55.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.664][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:55.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:55.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.674][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:55.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:55.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:55.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:55.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.698][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:52:55.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:55.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.711][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:52:55.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:55.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:55.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:55.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:55.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:55.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:55.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:55.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:55.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.812][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:52:55.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:55.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.844][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 01:52:55.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:55.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:55.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:55.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:55.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:55.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:55.918][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:52:55.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:55.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:55.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:56.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:56.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:56.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:56.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:56.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:56.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:56.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:56.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:56.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:56.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.466][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.488][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:56.610][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-17 01:52:56.616][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:52:56.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:52:56.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.626][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:52:56.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:52:56.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.645][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:52:56.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:52:56.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.657][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:52:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:52:56.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.914][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:56.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:56.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:56.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:56.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:56.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.097][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:57.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:57.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.117][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:57.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:57.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:57.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:57.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.293][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.295][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.307][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:57.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:57.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:57.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:57.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:57.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:57.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.455][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:57.457][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:57.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.471][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:57.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.575][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.596][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.599][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.618][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:57.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:57.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:57.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:57.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:57.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.720][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:57.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:57.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.740][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:57.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:57.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.747][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:57.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:57.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.883][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.896][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.901][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:57.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:57.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:57.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:57.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:57.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.002][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.023][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.052][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.069][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.074][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.087][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.132][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:58.146][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:58.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.151][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.182][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:58.201][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:58.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.207][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.232][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:58.243][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:58.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.270][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:58.272][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:58.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.289][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.310][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:58.313][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:58.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.330][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.354][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.357][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:58.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.375][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:52:58.402][biodb::testThat]
biodb.INFO [2024-10-17 01:52:58.407][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-17 01:52:58.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:58.412][biodb::testThat]
biodb.DEBUG[2024-10-17 01:52:58.504][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-10-17 01:52:58.532][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:52:58.558][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-10-17 01:52:58.561][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:58.596][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-10-17 01:52:58.599][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:52:58.753][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:52:58.756][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 01:52:58.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:58.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:58.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:58.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:58.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:58.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:58.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:52:58.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:58.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:58.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:58.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:58.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:58.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:58.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:58.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:58.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.973][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:52:58.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:52:58.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:58.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:58.997][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:59.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:59.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:59.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:59.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.059][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:59.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:52:59.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:59.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:59.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:59.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:52:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.124][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:52:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:59.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.149][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:52:59.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:59.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.169][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:59.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:59.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:59.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:59.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.264][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:52:59.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.282][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 01:52:59.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.322][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:52:59.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.424][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.471][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:59.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:59.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.495][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:59.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:59.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:59.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:59.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:52:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:59.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:59.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:59.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:59.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:59.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:59.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:59.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:59.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:59.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:59.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:59.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:59.716][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-17 01:52:59.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-17 01:52:59.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-17 01:52:59.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-17 01:52:59.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-17 01:52:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:59.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-17 01:52:59.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-17 01:52:59.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:52:59.838][biodb::testThat]
biodb.INFO [2024-10-17 01:52:59.840][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-17 01:52:59.853][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:59.856][biodb::testThat]
biodb.TRACE[2024-10-17 01:52:59.874][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:59.878][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:59.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:59.884][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:59.897][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-10-17 01:53:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:00.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:00.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:00.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:00.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:00.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:00.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:00.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:00.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:00.134][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 01:53:00.191][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[2024-10-17 01:53:00.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:00.333][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:00.350][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-10-17 01:53:01.349][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-10-17 01:53:01.748][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:01.751][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-10-17 01:53:01.778][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-10-17 01:53:01.782][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-10-17 01:53:01.801][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:01.806][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:01.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:01.809][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:53:01.815][biodb::testThat]
biodb.INFO [2024-10-17 01:53:01.817][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-17 01:53:01.819][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:01.821][biodb::testThat]
biodb.TRACE[2024-10-17 01:53:01.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:01.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:01.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:01.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:01.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:01.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:01.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:01.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:01.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:01.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:01.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:01.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:02.217][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 01:53:02.228][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:53:02.272][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-17 01:53:02.274][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:53:02.276][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-10-17 01:53:02.305][biodb::testThat]
biodb.INFO [2024-10-17 01:53:02.310][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-17 01:53:02.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:02.314][biodb::testThat]
biodb.TRACE[2024-10-17 01:53:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:02.364][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:02.370][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:53:02.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:53:02.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:02.379][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:53:02.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:53:02.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:02.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:02.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:53:02.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:02.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:53:02.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:53:02.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:02.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:53:02.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:53:02.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:02.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:53:02.557][biodb::testThat]
biodb.INFO [2024-10-17 01:53:02.558][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-17 01:53:02.559][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:02.560][biodb::testThat]
biodb.INFO [2024-10-17 01:53:02.576][biodb::testThat]
biodb.INFO [2024-10-17 01:53:02.577][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-17 01:53:02.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:02.580][biodb::testThat]
biodb.INFO [2024-10-17 01:53:02.594][biodb::testThat]
biodb.INFO [2024-10-17 01:53:02.595][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-17 01:53:02.600][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:02.601][biodb::testThat]
biodb.DEBUG[2024-10-17 01:53:02.606][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-10-17 01:53:03.121][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-10-17 01:53:03.522][biodb::testThat]
biodb.INFO [2024-10-17 01:53:03.536][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-17 01:53:03.539][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:03.541][biodb::testThat]
biodb.TRACE[2024-10-17 01:53:03.583][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:03.586][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:03.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:03.590][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:03.610][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:03.613][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:03.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:03.617][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:53:03.634][biodb::testThat]
biodb.INFO [2024-10-17 01:53:03.636][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-17 01:53:03.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:03.650][biodb::testThat]
biodb.TRACE[2024-10-17 01:53:03.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:03.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:03.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:03.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:03.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:03.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:03.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:03.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:03.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:03.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:03.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:03.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:04.018][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 01:53:04.047][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:53:04.050][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-17 01:53:04.053][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:53:04.062][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-10-17 01:53:04.386][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-17 01:53:04.403][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:53:04.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-17 01:53:04.428][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:53:04.431][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-10-17 01:53:04.530][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:53:04.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:53:04.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:04.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:04.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:04.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:04.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:04.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:04.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:04.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:04.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:04.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:04.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:04.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:04.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:04.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:04.801][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-10-17 01:53:04.895][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:04.897][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:04.978][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-10-17 01:53:05.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-10-17 01:53:12.316][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:12.328][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-10-17 01:53:12.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-10-17 01:53:17.241][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[2024-10-17 01:53:17.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:17.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:17.255][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-10-17 01:53:17.643][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-10-17 01:53:18.005][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:18.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-10-17 01:53:18.020][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-10-17 01:53:18.090][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-10-17 01:53:18.109][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:18.112][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:53:18.125][rule$waitAsNeeded] Wait 0.138841 second(s).
biodb.TRACE[2024-10-17 01:53:18.385][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-10-17 01:53:18.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-10-17 01:53:19.165][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:19.183][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-10-17 01:53:19.202][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-10-17 01:53:19.263][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:19.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:19.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:53:19.295][biodb::testThat]
biodb.INFO [2024-10-17 01:53:19.297][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-17 01:53:19.299][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:19.302][biodb::testThat]
biodb.TRACE[2024-10-17 01:53:19.309][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:53:19.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:53:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:19.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:19.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:19.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:19.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:19.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:19.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:19.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:19.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:19.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:19.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:19.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:19.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:19.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:19.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:19.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:19.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:19.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:19.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:19.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:19.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:19.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:53:19.474][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-17 01:53:19.497][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:19.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:19.510][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-10-17 01:53:20.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-10-17 01:53:25.416][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:25.421][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-10-17 01:53:25.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-10-17 01:53:29.333][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-10-17 01:53:29.600][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-17 01:53:29.615][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-10-17 01:53:29.618][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-17 01:53:29.621][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:53:29.635][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:53:29.637][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 01:53:29.642][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:53:29.644][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:53:29.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:29.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:29.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:29.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:29.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:29.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:29.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:53:29.785][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-10-17 01:53:29.803][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:29.805][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:29.808][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-10-17 01:53:30.159][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-10-17 01:53:30.485][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:30.489][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-10-17 01:53:30.497][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-10-17 01:53:30.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:30.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:30.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:30.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:30.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:30.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:30.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:53:30.525][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-10-17 01:53:30.531][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:30.534][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:53:30.536][rule$waitAsNeeded] Wait 0.271546 second(s).
biodb.TRACE[2024-10-17 01:53:30.952][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-10-17 01:53:31.278][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-10-17 01:53:31.612][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:31.617][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-10-17 01:53:31.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-10-17 01:53:31.628][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-10-17 01:53:31.631][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:53:31.634][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-17 01:53:31.641][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 01:53:31.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:31.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:31.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:31.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:31.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:31.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:31.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:31.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:31.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:31.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:31.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:31.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:31.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:31.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:31.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:31.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:53:31.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:53:31.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:31.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:31.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:53:31.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:53:31.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:31.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:31.855][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:53:31.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:53:31.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:31.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:31.929][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:53:31.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:53:31.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:31.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:31.950][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:31.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:31.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:31.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:31.994][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:32.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:32.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:32.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:32.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:32.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:32.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:53:32.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:32.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.143][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:53:32.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:32.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.153][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:53:32.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:53:32.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:53:32.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:53:32.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:32.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:32.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:32.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:32.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.481][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:53:32.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 01:53:32.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:32.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:32.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:32.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:32.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:32.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.657][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:53:32.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:32.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:32.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:32.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.839][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:32.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:32.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:32.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:32.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.921][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:32.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:32.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:32.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:32.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:32.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:33.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:33.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:33.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:33.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:33.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:33.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:33.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:33.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:53:33.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:53:33.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.346][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:53:33.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:53:33.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.379][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:53:33.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:53:33.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:33.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:33.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:33.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:53:33.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:33.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:33.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:33.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:53:33.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.536][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:53:33.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:33.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.546][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:53:33.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:33.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:53:33.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:53:33.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:53:33.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:53:33.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:33.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:33.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:33.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:33.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.658][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:53:33.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:33.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.686][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 01:53:33.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:33.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:33.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:33.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:53:33.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:33.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.722][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:53:33.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:53:33.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.731][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:33.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:33.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.754][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:33.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:33.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.783][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:33.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:33.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:33.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:53:33.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:53:33.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:33.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:33.956][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-10-17 01:53:33.992][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:53:33.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:33.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:34.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:34.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:34.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:34.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:34.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.045][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.047][private$selectFields]
biodb.TRACE[2024-10-17 01:53:34.049][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:34.055][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:34.057][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.059][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.063][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.074][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.087][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.089][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.093][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.095][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.098][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.140][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.144][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.150][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.153][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:34.155][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.174][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.185][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.231][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-17 01:53:34.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:34.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:34.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:34.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:34.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:34.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:34.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:34.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.307][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.323][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.325][private$selectFields]
biodb.TRACE[2024-10-17 01:53:34.328][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:34.330][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:34.332][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.334][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.336][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.345][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.347][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.352][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.362][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.364][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.366][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.369][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.386][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.388][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:34.405][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.433][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.451][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.467][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-17 01:53:34.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:34.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:34.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:34.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:34.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:34.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:34.496][FUN] Functions in observer BiodbConfig: [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[2024-10-17 01:53:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.508][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.549][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.550][private$selectFields]
biodb.TRACE[2024-10-17 01:53:34.551][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:34.553][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:34.554][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.555][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.557][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.560][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.562][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.564][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.579][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.581][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.584][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:34.586][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.589][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.593][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.595][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:34.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.614][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.625][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:34.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.639][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-17 01:53:34.641][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:53:34.644][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:53:34.729][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:34.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:34.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:53:34.778][biodb::testThat]
biodb.INFO [2024-10-17 01:53:34.780][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-17 01:53:34.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:34.802][biodb::testThat]
biodb.TRACE[2024-10-17 01:53:34.874][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:53:34.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:53:34.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:34.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:34.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:34.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:34.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:34.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:34.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:34.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:34.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:34.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:34.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:35.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:35.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:35.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:35.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:35.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:35.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:35.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:35.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:35.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:35.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:35.415][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[2024-10-17 01:53:35.434][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[2024-10-17 01:53:35.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:35.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:35.460][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-10-17 01:53:35.982][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-10-17 01:53:41.700][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:53:41.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-10-17 01:53:42.027][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-10-17 01:53:45.411][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:53:45.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:45.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:45.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:45.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:45.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:45.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:45.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:45.729][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:45.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:45.756][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:45.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:45.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:45.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:45.937][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:45.954][private$selectFields]
biodb.TRACE[2024-10-17 01:53:45.956][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:45.958][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:45.960][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:45.962][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:45.977][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:45.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:45.982][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:45.984][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.001][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.007][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.009][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.089][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.102][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.104][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.108][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.122][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:46.124][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.146][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.165][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.198][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-17 01:53:46.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:46.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:46.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:46.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:46.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:46.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:46.270][FUN] Functions in observer BiodbConfig: [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[2024-10-17 01:53:46.273][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.299][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.322][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.324][private$selectFields]
biodb.TRACE[2024-10-17 01:53:46.341][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:46.344][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:46.346][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.348][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.351][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.367][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.380][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.384][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.388][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.400][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.403][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.406][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.417][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.421][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.423][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:46.426][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.456][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.498][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.526][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-17 01:53:46.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:46.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:46.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:46.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:46.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:46.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:46.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:46.575][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.609][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.634][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.636][private$selectFields]
biodb.TRACE[2024-10-17 01:53:46.639][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:46.653][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:46.656][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.659][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.662][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.683][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.687][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.701][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.706][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.708][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.723][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:46.726][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.729][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.746][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.749][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:46.751][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.773][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.810][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:46.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:46.835][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-17 01:53:46.837][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:53:46.840][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:53:46.898][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:46.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:46.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:53:46.942][biodb::testThat]
biodb.INFO [2024-10-17 01:53:46.944][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-17 01:53:46.960][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:46.963][biodb::testThat]
biodb.TRACE[2024-10-17 01:53:46.983][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:53:46.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:53:46.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:47.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:47.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:47.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:53:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:47.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:47.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:47.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:47.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:47.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:47.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:47.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:53:47.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:47.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:53:47.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:47.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:47.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:47.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:47.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:47.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:47.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:53:47.705][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-17 01:53:47.727][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:53:47.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-10-17 01:53:47.748][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:53:47.848][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-10-17 01:53:52.406][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:53:52.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:52.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:52.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:52.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:52.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:52.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:52.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.493][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.495][private$selectFields]
biodb.TRACE[2024-10-17 01:53:52.497][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:52.508][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:52.511][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.514][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.516][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.532][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.534][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.537][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.548][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.551][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.553][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.567][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.570][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.575][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.586][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:52.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.598][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.639][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-17 01:53:52.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:52.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:52.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:52.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:52.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:52.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:52.695][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.TRACE[2024-10-17 01:53:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.719][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.739][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.741][private$selectFields]
biodb.TRACE[2024-10-17 01:53:52.743][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:52.746][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:52.759][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.761][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.764][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.779][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.781][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.786][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.801][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.804][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.806][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:52.808][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.823][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.828][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.830][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:52.842][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.884][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.906][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-17 01:53:52.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:52.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:52.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:52.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:52.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:52.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:52.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:53:52.965][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:52.987][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:52.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:52.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:53.008][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:53.010][private$selectFields]
biodb.TRACE[2024-10-17 01:53:53.013][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:53:53.015][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:53:53.029][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:53.031][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.034][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:53.048][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:53.050][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.053][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:53.057][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:53.067][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:53.069][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:53:53.071][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.074][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:53.093][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:53.096][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-17 01:53:53.098][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:53.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:53.109][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:53.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:53.130][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:53:53.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:53.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:53:53.152][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-17 01:53:53.164][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:53:53.166][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:53:53.272][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:53.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:53:53.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:53:53.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:53:53.311][biodb::testThat]
biodb.INFO [2024-10-17 01:53:53.314][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-17 01:53:53.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:53:53.329][biodb::testThat]
biodb.DEBUG[2024-10-17 01:53:53.334][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-17 01:53:53.346][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:53:53.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-17 01:53:53.354][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:53:53.357][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:53:53.372][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:53:53.376][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 01:53:53.379][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:53:53.394][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:53:53.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:53:53.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:53:53.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:53:53.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:53:53.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:53:53.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:53:53.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:53:53.546][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-10-17 01:53:53.553][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:53.556][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:53.570][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:53:53.918][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:53:53.920][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:53:53.923][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:53:53.927][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:53:54.468][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:53:54.471][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:54.474][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:53:54.477][rule$waitAsNeeded] Wait 0.0929821 second(s).
biodb.TRACE[2024-10-17 01:53:54.575][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:53:54.901][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:53:54.903][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:53:54.906][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[2024-10-17 01:53:54.910][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:53:55.525][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:53:55.528][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:55.530][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:53:55.533][rule$waitAsNeeded] Wait 0.041791 second(s).
biodb.TRACE[2024-10-17 01:53:55.619][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:53:56.095][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:53:56.097][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:53:56.099][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:53:56.102][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:53:56.666][private$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[2024-10-17 01:53:56.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:56.671][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:53:56.674][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:53:57.000][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:53:57.002][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:53:57.005][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:53:57.007][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:53:57.344][private$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[2024-10-17 01:53:57.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:57.349][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:53:57.353][rule$waitAsNeeded] Wait 0.321544 second(s).
biodb.TRACE[2024-10-17 01:53:57.809][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:53:58.150][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:53:58.179][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:53:58.182][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[2024-10-17 01:53:58.183][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:53:58.525][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:53:58.527][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:58.530][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:53:58.537][rule$waitAsNeeded] Wait 0.275443 second(s).
biodb.TRACE[2024-10-17 01:53:58.817][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:53:59.143][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:53:59.146][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:53:59.148][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:53:59.150][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:53:59.481][private$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[2024-10-17 01:53:59.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:53:59.487][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:53:59.490][rule$waitAsNeeded] Wait 0.326739 second(s).
biodb.TRACE[2024-10-17 01:53:59.823][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:54:00.151][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:00.153][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:00.156][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[2024-10-17 01:54:00.158][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:54:00.632][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:54:00.636][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:00.646][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:00.650][rule$waitAsNeeded] Wait 0.17312 second(s).
biodb.TRACE[2024-10-17 01:54:00.830][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:54:01.156][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:01.159][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:01.162][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:54:01.165][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:54:01.757][private$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[2024-10-17 01:54:01.760][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:01.775][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:01.780][rule$waitAsNeeded] Wait 0.051435 second(s).
biodb.TRACE[2024-10-17 01:54:01.836][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:54:02.193][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:02.222][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:02.225][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[2024-10-17 01:54:02.227][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:54:02.983][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:54:02.986][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:02.988][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:02.991][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-17 01:54:03.316][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:03.318][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:03.319][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[2024-10-17 01:54:03.320][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-17 01:54:03.896][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-10-17 01:54:04.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-10-17 01:54:04.005][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:54:04.006][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:54:04.008][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 01:54:04.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:04.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:04.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:04.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:04.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:04.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:04.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:54:04.029][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:04.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:04.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:04.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:04.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:04.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:04.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:04.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:04.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:04.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:04.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:04.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:04.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:04.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:04.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:04.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:04.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:04.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:04.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:04.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:04.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:04.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:04.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:04.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:04.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:54:04.083][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-10-17 01:54:04.085][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-17 01:54:04.100][biodb::testThat]
biodb.INFO [2024-10-17 01:54:04.101][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-17 01:54:04.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:04.112][biodb::testThat]
biodb.DEBUG[2024-10-17 01:54:04.133][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-10-17 01:54:04.135][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-10-17 01:54:04.136][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-17 01:54:04.145][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-10-17 01:54:04.149][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-17 01:54:04.160][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:54:04.162][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:54:04.165][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 01:54:04.167][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:54:04.175][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:54:04.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:04.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:04.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:04.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:04.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:04.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:04.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:04.220][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-10-17 01:54:04.227][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:04.229][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:04.232][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:04.577][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:04.578][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:04.580][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:54:04.581][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:04.909][private$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[2024-10-17 01:54:04.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:04.914][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:04.916][rule$waitAsNeeded] Wait 0.315866 second(s).
biodb.TRACE[2024-10-17 01:54:05.377][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:05.716][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:05.717][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:05.719][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[2024-10-17 01:54:05.721][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:06.251][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:54:06.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:06.256][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:06.259][rule$waitAsNeeded] Wait 0.117629 second(s).
biodb.TRACE[2024-10-17 01:54:06.524][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:06.857][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:06.859][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:06.861][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:54:06.864][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:07.349][private$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[2024-10-17 01:54:07.351][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:07.353][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:07.356][rule$waitAsNeeded] Wait 0.1673 second(s).
biodb.TRACE[2024-10-17 01:54:07.564][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:07.890][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:07.892][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:07.895][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[2024-10-17 01:54:07.897][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:08.322][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:54:08.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:08.327][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:08.330][rule$waitAsNeeded] Wait 0.233348 second(s).
biodb.TRACE[2024-10-17 01:54:08.567][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:08.920][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:08.921][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:08.923][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:54:08.925][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:09.259][private$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[2024-10-17 01:54:09.261][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:09.263][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:09.266][rule$waitAsNeeded] Wait 0.300976 second(s).
biodb.TRACE[2024-10-17 01:54:09.689][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:10.013][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:10.014][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:10.017][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[2024-10-17 01:54:10.018][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:10.349][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:54:10.351][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:10.354][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:10.357][rule$waitAsNeeded] Wait 0.331632 second(s).
biodb.TRACE[2024-10-17 01:54:10.818][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:11.143][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:11.146][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:11.148][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:54:11.151][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:11.656][private$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[2024-10-17 01:54:11.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:11.668][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:11.674][rule$waitAsNeeded] Wait 0.129379 second(s).
biodb.TRACE[2024-10-17 01:54:11.818][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:12.201][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:12.203][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:12.204][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[2024-10-17 01:54:12.205][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:12.576][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-17 01:54:12.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:12.582][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:12.586][rule$waitAsNeeded] Wait 0.231333 second(s).
biodb.TRACE[2024-10-17 01:54:12.966][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:13.309][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:13.313][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:13.319][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:54:13.325][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:14.074][private$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[2024-10-17 01:54:14.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:14.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:14.079][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-17 01:54:14.412][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-17 01:54:14.414][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-17 01:54:14.416][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-17 01:54:14.418][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-17 01:54:15.099][private$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[2024-10-17 01:54:15.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:15.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:15.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:15.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:15.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:15.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:15.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:15.157][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-10-17 01:54:15.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:15.168][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:15.171][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-10-17 01:54:15.501][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2024-10-17 01:54:15.849][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:15.854][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2024-10-17 01:54:15.866][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2024-10-17 01:54:15.873][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-10-17 01:54:15.884][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:54:15.887][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-17 01:54:15.889][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 01:54:15.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:15.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:15.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:15.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:15.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:15.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:15.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:54:15.968][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:15.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:15.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:15.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:15.976][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:15.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:15.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:15.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:15.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:15.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:15.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:15.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:54:15.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:15.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:16.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:16.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:16.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:16.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:16.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:54:16.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:16.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:16.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:16.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:16.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:16.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:16.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:16.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:16.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.195][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:16.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:16.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.208][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:16.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:16.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.230][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:16.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:16.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.280][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:16.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:16.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:16.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.463][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:16.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:16.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:16.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:16.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:16.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.524][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:54:16.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:16.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.552][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:54:16.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:16.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:16.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:16.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:16.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.651][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:54:16.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.668][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 01:54:16.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.732][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:54:16.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:16.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:16.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.866][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:16.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:16.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:16.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:16.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:16.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.938][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:16.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:16.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:16.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:16.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:16.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:16.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:17.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:17.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:17.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:17.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:54:17.169][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2024-10-17 01:54:17.171][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-17 01:54:17.176][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-17 01:54:17.232][biodb::testThat]
biodb.INFO [2024-10-17 01:54:17.234][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-17 01:54:17.237][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:17.239][biodb::testThat]
biodb.INFO [2024-10-17 01:54:17.387][biodb::testThat]
biodb.INFO [2024-10-17 01:54:17.389][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-17 01:54:17.392][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:17.399][biodb::testThat]
biodb.INFO [2024-10-17 01:54:17.431][biodb::testThat]
biodb.INFO [2024-10-17 01:54:17.433][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-17 01:54:17.436][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:17.438][biodb::testThat]
biodb.DEBUG[2024-10-17 01:54:17.464][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-17 01:54:17.472][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:17.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:17.496][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-10-17 01:54:18.033][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-10-17 01:54:25.661][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:25.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-10-17 01:54:26.039][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-10-17 01:54:30.828][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:30.840][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:30.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:30.843][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:30.845][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:30.846][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:30.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:30.848][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:54:30.850][biodb::testThat]
biodb.INFO [2024-10-17 01:54:30.855][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-17 01:54:30.857][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:30.858][biodb::testThat]
biodb.ERROR[2024-10-17 01:54:30.904][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-17 01:54:31.020][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-17 01:54:31.059][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:54:31.062][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-17 01:54:31.065][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-17 01:54:31.067][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:54:31.086][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:31.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:31.091][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:31.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:31.105][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.137][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.INFO [2024-10-17 01:54:31.244][biodb::testContext]
biodb.INFO [2024-10-17 01:54:31.250][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:54:31.254][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-10-17 01:54:31.259][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:54:31.274][biodb::testContext]
biodb.INFO [2024-10-17 01:54:31.297][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:54:31.308][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:54:31.324][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:54:31.327][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:54:31.332][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:54:31.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.341][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:54:31.356][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:54:31.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.373][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:54:31.375][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:54:31.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.413][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:54:31.427][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:54:31.431][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:54:31.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.448][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:54:31.450][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:54:31.453][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:54:31.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.478][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:54:31.480][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:54:31.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.505][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:54:31.520][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:54:31.523][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:54:31.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.544][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:54:31.546][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:54:31.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.569][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:54:31.571][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:54:31.584][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:54:31.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.593][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:54:31.615][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:54:31.617][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:54:31.620][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:54:31.623][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:54:31.642][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:54:31.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.673][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:54:31.685][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:54:31.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.698][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:54:31.700][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:54:31.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.720][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:54:31.723][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:54:31.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.742][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:54:31.751][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:54:31.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.760][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:54:31.773][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:54:31.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.786][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:54:31.789][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:54:31.811][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:54:31.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.819][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:54:31.834][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:54:31.848][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:54:31.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:31.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:31.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:31.867][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:54:31.881][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:31.884][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 01:54:31.886][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:31.900][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:31.903][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:31.906][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:31.908][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:31.934][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:31.936][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:54:31.939][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:31.942][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:31.955][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:54:31.957][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:31.981][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:31.983][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:31.986][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:54:31.986][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:54:31.986][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:54:31.986][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:54:31.986][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:54:32.006][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:32.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:32.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:32.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:32.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:32.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:32.052][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.068][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.082][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:32.088][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:32.091][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.094][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.108][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:54:32.112][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.115][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:54:32.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:32.123][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.125][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.129][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.131][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:54:32.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:32.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.139][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:54:32.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:32.145][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.149][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.152][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:54:32.152][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:54:32.152][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:54:32.152][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:54:32.152][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:54:32.155][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:32.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:32.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:32.237][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:32.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:32.241][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:32.245][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.247][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.250][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:32.263][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:32.265][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.268][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.271][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:54:32.276][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.279][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 01:54:32.283][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.285][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:32.290][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.294][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.297][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.299][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.333][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:54:32.336][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:32.340][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.343][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:54:32.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:32.349][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.353][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.356][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.359][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:32.361][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:32.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:32.397][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:32.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:32.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:32.407][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.412][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.419][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:32.429][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:32.473][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.490][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.493][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:54:32.512][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.544][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:54:32.547][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.549][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:32.573][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.579][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:32.601][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:54:32.623][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:32.672][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:32.702][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:54:32.724][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:32.776][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:32.906][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:32.912][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:32.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:32.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:32.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:33.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:33.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:33.018][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:33.021][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:33.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:33.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:33.048][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:33.062][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:33.078][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:54:33.098][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.209][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.DEBUG[2024-10-17 01:54:33.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.269][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[2024-10-17 01:54:33.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.307][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:54:33.311][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:54:33.313][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:54:33.318][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:54:33.321][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:54:33.324][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:54:33.331][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:54:33.334][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:54:33.337][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:54:33.341][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:54:33.346][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:54:33.351][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:54:33.354][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:54:33.357][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:54:33.371][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:54:33.373][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:54:33.376][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:54:33.378][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:54:33.381][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:54:33.383][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:54:33.386][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:54:33.388][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:54:33.391][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:54:33.394][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:54:33.398][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:54:33.401][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:54:33.404][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:54:33.406][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:54:33.408][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:54:33.410][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:54:33.412][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:54:33.416][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:54:33.431][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:54:33.434][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:54:33.437][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:54:33.455][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:54:33.458][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:54:33.461][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:54:33.462][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:54:33.464][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:54:33.470][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:54:33.472][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:54:33.474][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:54:33.475][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:54:33.477][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:54:33.482][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:54:33.485][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:54:33.489][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:54:33.492][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:54:33.495][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:54:33.497][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:54:33.499][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:54:33.501][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:54:33.504][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:54:33.507][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:54:33.510][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:54:33.513][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:54:33.517][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:54:33.520][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:54:33.522][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:54:33.525][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:54:33.528][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:54:33.536][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:54:33.539][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:54:33.542][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:54:33.552][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:54:33.555][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:54:33.558][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:54:33.565][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:54:33.568][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:54:33.570][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:54:33.573][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:54:33.576][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:54:33.581][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:54:33.584][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:54:33.587][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:54:33.591][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:54:33.594][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:54:33.598][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:54:33.602][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:54:33.605][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:54:33.609][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:54:33.612][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:54:33.615][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:54:33.619][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:54:33.701][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:54:33.703][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.707][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.928][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[2024-10-17 01:54:33.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:33.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:33.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:33.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:33.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:33.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:33.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:33.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:34.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:34.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:34.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:34.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:34.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:34.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:34.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:34.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:34.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:34.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:34.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:34.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:34.028][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-17 01:54:34.032][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:54:34.038][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:34.040][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:54:34.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:34.045][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:34.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:34.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:34.058][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:34.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:34.062][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:54:34.064][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:34.066][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:34.069][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-17 01:54:34.071][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-17 01:54:34.073][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-17 01:54:34.075][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:34.078][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:54:34.078][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:54:34.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:34.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:34.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:34.090][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:34.092][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:34.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:34.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:34.099][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 01:54:34.099][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-17 01:54:34.105][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:34.106][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:34.109][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:34.111][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:34.115][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-17 01:54:34.127][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:54:34.209][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:54:34.211][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-17 01:54:34.232][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:54:34.236][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-17 01:54:34.279][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 01:54:34.286][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 01:54:34.290][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-17 01:54:34.292][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-17 01:54:34.295][biodb::testThat]
biodb.INFO [2024-10-17 01:54:34.299][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-10-17 01:54:34.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:34.305][biodb::testThat]
biodb.DEBUG[2024-10-17 01:54:34.314][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[2024-10-17 01:54:34.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:34.325][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:34.327][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-10-17 01:54:34.692][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-10-17 01:54:35.057][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:35.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-10-17 01:54:35.074][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-10-17 01:54:35.096][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-10-17 01:54:35.104][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:35.106][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:35.109][rule$waitAsNeeded] Wait 0.217898 second(s).
biodb.TRACE[2024-10-17 01:54:35.378][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-10-17 01:54:35.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-10-17 01:54:36.146][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:36.150][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-10-17 01:54:36.160][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-10-17 01:54:36.196][biodb::testThat]
biodb.INFO [2024-10-17 01:54:36.199][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-10-17 01:54:36.202][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:36.206][biodb::testThat]
biodb.INFO [2024-10-17 01:54:36.445][biodb::testThat]
biodb.INFO [2024-10-17 01:54:36.447][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-10-17 01:54:36.448][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:36.450][biodb::testThat]
biodb.DEBUG[2024-10-17 01:54:36.455][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-17 01:54:36.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:36.465][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:36.469][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-10-17 01:54:36.824][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-10-17 01:54:37.155][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:37.160][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-10-17 01:54:37.169][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-10-17 01:54:37.184][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[2024-10-17 01:54:37.191][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:54:37.195][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-10-17 01:54:37.198][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:54:37.201][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-10-17 01:54:37.215][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[2024-10-17 01:54:37.222][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:37.224][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:37.227][rule$waitAsNeeded] Wait 0.241021 second(s).
biodb.TRACE[2024-10-17 01:54:37.543][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-10-17 01:54:37.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-10-17 01:54:38.216][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:38.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-10-17 01:54:38.231][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-10-17 01:54:38.275][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[2024-10-17 01:54:38.288][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:38.291][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 01:54:38.294][rule$waitAsNeeded] Wait 0.247821 second(s).
biodb.TRACE[2024-10-17 01:54:38.676][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-10-17 01:54:39.180][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-10-17 01:54:40.704][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:40.708][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-10-17 01:54:40.764][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-10-17 01:54:41.524][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[2024-10-17 01:54:41.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:54:41.536][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:54:41.546][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-10-17 01:54:42.052][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-10-17 01:54:43.503][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:54:43.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-10-17 01:54:43.569][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-10-17 01:54:44.421][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:54:44.434][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-17 01:54:44.437][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-17 01:54:44.440][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:54:44.442][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:44.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:44.457][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:44.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:44.462][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 01:54:44.495][biodb::testContext]
biodb.INFO [2024-10-17 01:54:44.497][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:54:44.500][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-10-17 01:54:44.513][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:54:44.517][biodb::testContext]
biodb.INFO [2024-10-17 01:54:44.533][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:54:44.538][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:54:44.570][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:54:44.573][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:54:44.577][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:54:44.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.610][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:54:44.614][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:54:44.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.636][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:54:44.639][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:54:44.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.659][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[2024-10-17 01:54:44.663][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:54:44.688][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:54:44.691][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:54:44.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.714][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:54:44.717][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:54:44.732][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:54:44.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.752][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:54:44.755][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:54:44.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.777][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:54:44.779][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:54:44.790][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:54:44.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.810][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:54:44.813][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:54:44.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.832][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:54:44.834][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:54:44.837][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:54:44.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.856][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[2024-10-17 01:54:44.859][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:54:44.873][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:54:44.876][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:54:44.879][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:54:44.882][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:54:44.911][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:54:44.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.935][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:54:44.946][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:54:44.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.955][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:54:44.971][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:54:44.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:44.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:44.989][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:54:44.992][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:54:44.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:44.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.024][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:54:45.027][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:54:45.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.044][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:54:45.047][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:54:45.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.067][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:54:45.069][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:54:45.139][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:54:45.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.147][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:54:45.150][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:54:45.152][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:54:45.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.159][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:54:45.166][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.168][self$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[2024-10-17 01:54:45.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.171][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:45.173][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.176][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.179][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.181][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.183][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:54:45.185][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:45.187][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.189][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:54:45.192][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:45.194][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.196][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.197][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:54:45.197][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:54:45.197][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:54:45.197][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:54:45.197][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:54:45.199][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:45.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:45.206][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.210][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.212][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:45.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:45.218][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.221][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.225][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:54:45.229][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.231][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:54:45.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.241][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:45.243][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.245][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.247][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.249][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.252][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:54:45.254][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:45.257][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.259][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:54:45.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:45.270][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.273][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.275][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:54:45.275][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:54:45.275][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:54:45.275][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:54:45.275][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:54:45.278][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:45.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.290][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:45.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.294][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.296][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.299][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:45.313][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:45.315][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.317][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.320][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:54:45.325][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.346][self$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[2024-10-17 01:54:45.349][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.351][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:45.353][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.358][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.360][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.367][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:54:45.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:45.372][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.374][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:54:45.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:45.377][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.379][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.381][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:45.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:45.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.395][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:45.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:45.407][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.409][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.412][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:54:45.416][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.419][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:54:45.421][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:45.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.435][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:54:45.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:45.439][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.440][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:54:45.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:45.443][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.456][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:45.458][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.461][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:45.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:45.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:45.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:45.477][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:45.478][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.479][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:45.480][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:45.487][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:45.489][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:45.490][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:54:45.492][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.674][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[2024-10-17 01:54:45.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.765][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[2024-10-17 01:54:45.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:45.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:45.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:45.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:45.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:45.837][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[2024-10-17 01:54:45.849][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:54:45.852][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:54:45.858][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:54:45.862][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:54:45.865][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:54:45.869][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:54:45.873][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:54:45.875][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:54:45.878][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:54:45.881][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:54:45.885][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:54:45.891][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:54:45.894][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:54:45.898][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:54:45.901][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:54:45.904][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:54:45.907][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:54:45.911][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:54:45.914][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:54:45.916][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:54:45.917][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:54:45.924][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:54:45.927][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:54:45.930][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:54:45.933][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:54:45.944][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:54:45.948][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:54:45.962][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:54:45.966][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:54:45.969][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:54:45.984][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:54:45.988][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:54:45.991][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:54:45.999][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:54:46.003][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:54:46.007][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:54:46.015][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:54:46.021][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:54:46.037][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:54:46.058][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:54:46.062][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:54:46.065][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:54:46.076][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:54:46.080][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:54:46.086][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:54:46.089][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:54:46.093][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:54:46.097][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:54:46.105][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:54:46.109][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:54:46.113][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:54:46.116][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:54:46.120][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:54:46.123][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:54:46.125][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:54:46.130][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:54:46.133][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:54:46.137][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:54:46.140][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:54:46.160][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:54:46.163][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:54:46.166][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:54:46.172][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:54:46.175][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:54:46.177][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:54:46.179][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:54:46.185][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:54:46.192][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:54:46.196][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:54:46.262][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:54:46.265][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:54:46.270][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:54:46.275][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:54:46.279][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:54:46.282][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:54:46.294][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:54:46.298][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:54:46.317][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:54:46.322][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:54:46.328][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:54:46.333][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:54:46.340][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:54:46.344][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:54:46.347][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:54:46.356][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:54:46.359][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:54:46.362][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.374][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.633][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[2024-10-17 01:54:46.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.648][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[2024-10-17 01:54:46.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.722][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[2024-10-17 01:54:46.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:54:46.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:46.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:46.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:46.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:46.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:46.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:54:46.782][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-17 01:54:46.784][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:54:46.797][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:46.798][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:54:46.800][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:46.802][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:54:46.805][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:46.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:54:46.812][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:46.814][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:54:46.817][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:54:46.820][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:54:46.822][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:46.825][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-17 01:54:46.833][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-17 01:54:46.837][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-17 01:54:46.839][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:54:46.841][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:54:46.841][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:54:46.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:54:46.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:46.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:46.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:54:46.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:54:46.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:54:46.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:54:46.860][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-17 01:54:46.860][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-17 01:54:46.862][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:54:46.864][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:54:46.866][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:54:46.868][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:54:46.876][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-17 01:54:46.880][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:54:46.915][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:54:46.917][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-17 01:54:46.920][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-17 01:54:46.922][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-17 01:54:46.924][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 01:54:46.925][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-17 01:54:46.927][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-17 01:54:46.956][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-17 01:54:46.958][biodb::testThat]
biodb.INFO [2024-10-17 01:54:46.959][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-10-17 01:54:46.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:54:46.969][biodb::testThat]
biodb.DEBUG[2024-10-17 01:54:46.973][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-17 01:54:46.984][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:54:46.986][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-10-17 01:54:46.988][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:54:47.630][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-10-17 01:54:53.216][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-10-17 01:54:53.254][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-17 01:54:53.258][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-10-17 01:54:53.262][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-10-17 01:54:53.267][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-10-17 01:54:53.270][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:54:53.273][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-17 01:54:53.276][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-17 01:54:53.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:53.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:53.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:53.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:53.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:53.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:53.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:54:53.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.360][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:53.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:53.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.370][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:53.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.379][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.389][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.407][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.418][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:54:53.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:53.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.429][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:54:53.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:53.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.439][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:53.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:53.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:53.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:53.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.473][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:54:53.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 01:54:53.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.507][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:54:53.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.550][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.559][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.579][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:54:53.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:53.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:53.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:53.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:53.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:53.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:53.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:54:53.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.668][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:54:53.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:54:53.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.688][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:53.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.701][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:53.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.708][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:54:53.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.714][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-17 01:54:53.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:53.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:53.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:53.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:53.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:53.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.769][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:54:53.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.778][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-17 01:54:53.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:53.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.800][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-17 01:54:53.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:53.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.810][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.840][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:53.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:53.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:53.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:53.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:53.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:54:53.995][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-10-17 01:54:54.000][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:54:54.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:54.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:54.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:54.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:54.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:54.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:54.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:54:54.030][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.042][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:54:54.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:54:54.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.066][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:54:54.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:54:54.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.076][private$selectFields] Fields none
biodb.TRACE[2024-10-17 01:54:54.079][private$selectFields]
biodb.TRACE[2024-10-17 01:54:54.081][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-17 01:54:54.084][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:54:54.086][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:54:54.088][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.096][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.104][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.109][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.114][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.116][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.119][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.125][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.128][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.133][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.140][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.143][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.146][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.152][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.154][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.157][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.161][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.164][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.167][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.172][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.175][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.178][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.187][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.190][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.194][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.199][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.204][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.209][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.211][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.215][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.220][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.222][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.225][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.230][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.232][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.239][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.241][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.243][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.248][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.250][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.257][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.259][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.262][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.266][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.268][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:54:54.270][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:54:54.272][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.275][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.280][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.285][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.293][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.295][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.302][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.304][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.307][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.313][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.316][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.318][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.324][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.327][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.334][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.337][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.344][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.347][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.350][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.356][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.359][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-10-17 01:54:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.442][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.545][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.608][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.619][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.659][private$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[2024-10-17 01:54:54.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:54:54.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:54.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:54.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:54.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:54.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:54.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:54:54.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.698][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:54:54.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.707][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:54:54.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:54:54.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:54:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:54:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.721][private$selectFields] Fields none
biodb.TRACE[2024-10-17 01:54:54.723][private$selectFields]
biodb.TRACE[2024-10-17 01:54:54.724][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-17 01:54:54.726][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:54:54.727][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:54:54.729][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.736][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.742][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.746][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.749][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.752][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.757][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.759][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.761][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.767][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.770][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.778][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.781][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.783][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.788][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.791][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.794][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.819][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.822][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.824][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.829][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.831][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.834][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.838][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.840][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.843][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.849][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.852][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.854][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.859][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.861][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.864][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.870][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.872][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.875][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.881][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.884][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.889][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.895][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.898][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:54.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.907][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.910][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.913][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:54.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.917][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.920][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:54:54.923][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-17 01:54:54.928][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:54.930][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:54.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.935][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.938][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:54.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.945][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.948][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.951][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:54.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.957][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.961][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.964][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:54.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.969][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.973][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:54.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.979][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.984][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:54.987][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:54.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:54.992][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:54.996][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:54.999][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:55.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.003][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.007][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.010][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.015][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.019][private$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[2024-10-17 01:54:55.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:55.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:55.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:55.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:55.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:54:55.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:54:55.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:55.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:55.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:55.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:55.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:54:55.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:54:55.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:55.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:55.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:55.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.119][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:55.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:54:55.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:55.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:55.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:55.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:54:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:55.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:55.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:55.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:55.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:54:55.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:55.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.219][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:55.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:55.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:54:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:54:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:55.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:55.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:55.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:55.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:54:55.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:54:55.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.288][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.299][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-17 01:54:55.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:54:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:54:55.319][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-10-17 01:54:55.321][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:54:55.323][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-10-17 01:54:55.336][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:54:55.339][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-17 01:54:55.341][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-17 01:54:55.343][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:54:55.345][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:54:55.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:54:55.350][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:54:55.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:54:55.354][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:54:55.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 38.793   5.119 133.629

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn 5.045 1.93321.733
LipidmapsStructureEntry0.6170.0260.869