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This page was generated on 2024-10-18 20:38 -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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-10-16 22:08:38 -0400 (Wed, 16 Oct 2024)
EndedAt: 2024-10-16 22:11:26 -0400 (Wed, 16 Oct 2024)
EllapsedTime: 167.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-10-16 22:09:24.686][biodb::testContext]
biodb.INFO [2024-10-16 22:09:24.688][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:24.689][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-16 22:09:24.690][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:24.691][biodb::testContext]
biodb.INFO [2024-10-16 22:09:24.698][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:24.701][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:24.708][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:24.710][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:09:24.711][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:09:24.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.715][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:09:24.735][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:09:24.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.739][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:09:24.740][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:09:24.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.744][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:09:24.745][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:09:24.746][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:09:24.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.750][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:09:24.751][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:09:24.752][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:09:24.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.756][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:09:24.757][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:09:24.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.761][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:09:24.762][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:09:24.763][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:09:24.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.767][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:09:24.768][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:09:24.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.772][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:09:24.773][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:09:24.774][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:09:24.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.778][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:24.779][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:09:24.780][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:09:24.781][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:09:24.782][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:09:24.783][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:09:24.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.787][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:09:24.788][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:09:24.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.792][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:09:24.793][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:09:24.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.797][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:09:24.798][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:09:24.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.802][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:09:24.803][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:09:24.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.806][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:09:24.807][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:09:24.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.811][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:24.812][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:09:24.816][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:09:24.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.820][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:09:24.821][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:09:24.822][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:09:24.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:24.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.829][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:09:24.866][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.894][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:09:24.896][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:24.898][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.900][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.901][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.902][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.903][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:24.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:24.905][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.907][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:09:24.908][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:24.909][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.910][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.911][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:24.911][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:24.911][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:24.911][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:24.911][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:24.912][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:24.913][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:24.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:24.915][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:24.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:24.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:24.918][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.920][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.921][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:24.922][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:24.923][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.924][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.925][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:09:24.928][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.929][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:24.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:24.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.936][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:24.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:24.938][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.939][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:09:24.940][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:24.941][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:24.943][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:24.943][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:24.943][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:24.943][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:24.945][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:24.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:24.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:24.947][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:24.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:24.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:24.950][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.951][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.952][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:24.953][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:24.954][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.955][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.957][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:09:24.958][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.959][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:09:24.960][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.962][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:24.963][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.964][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.965][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.967][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:24.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:24.969][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.970][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:09:24.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:24.972][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.973][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.974][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.975][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:24.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:24.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:24.978][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:24.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:24.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:24.981][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.982][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:24.984][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:24.985][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.986][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:24.987][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:09:24.989][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.990][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:24.991][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.992][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:24.993][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:24.994][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.995][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:24.996][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:24.997][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:24.998][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:24.999][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:25.000][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:09:25.001][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:25.002][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:25.003][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:25.004][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:25.005][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:25.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:25.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:25.008][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:25.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:25.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:25.011][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:25.012][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:25.013][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:25.014][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:25.015][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:25.016][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:25.021][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:25.022][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.023][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.DEBUG[2024-10-16 22:09:25.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.101][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:09:25.106][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:09:25.108][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:09:25.109][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:09:25.110][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:25.112][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:25.113][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:25.115][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:25.116][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:09:25.117][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:25.119][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:25.120][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:09:25.122][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:25.123][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:25.124][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:09:25.126][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:25.127][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:09:25.128][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:09:25.130][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:25.131][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:09:25.133][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:09:25.134][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:09:25.135][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:09:25.137][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:09:25.138][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:09:25.140][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:09:25.141][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:09:25.142][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:09:25.144][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:09:25.145][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:09:25.147][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:09:25.148][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:09:25.149][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:09:25.151][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:09:25.152][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:09:25.153][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:09:25.155][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:09:25.156][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:09:25.168][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:09:25.169][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:09:25.171][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:09:25.172][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:09:25.173][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:09:25.175][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:09:25.176][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:09:25.177][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:09:25.179][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:09:25.180][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:09:25.181][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:09:25.183][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:09:25.184][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:09:25.185][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:09:25.186][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:09:25.188][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:09:25.189][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:09:25.190][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:09:25.191][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:09:25.193][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:09:25.194][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:09:25.195][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:09:25.197][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:09:25.198][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:09:25.199][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:09:25.200][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:09:25.202][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:09:25.203][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:09:25.204][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:25.205][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:25.207][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:09:25.208][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:09:25.209][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:09:25.211][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:09:25.212][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:09:25.213][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:09:25.214][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:09:25.216][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:09:25.217][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:09:25.218][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:09:25.220][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:09:25.221][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:09:25.222][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:09:25.223][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:09:25.225][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:09:25.230][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:09:25.232][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:25.235][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:25.236][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.238][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.248][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[2024-10-16 22:09:25.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.253][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[2024-10-16 22:09:25.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.288][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[2024-10-16 22:09:25.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.305][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[2024-10-16 22:09:25.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.334][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[2024-10-16 22:09:25.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:25.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.341][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:25.350][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:09:25.352][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:25.353][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:09:25.354][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:25.355][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:25.355][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:25.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:25.357][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:25.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:25.359][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:25.360][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:25.361][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:25.362][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-16 22:09:25.363][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-16 22:09:25.364][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-16 22:09:25.365][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:25.366][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:25.366][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:25.367][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:25.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:25.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:25.369][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:25.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:25.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:25.372][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:25.373][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 22:09:25.373][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-16 22:09:25.374][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:25.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:25.376][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:25.377][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:25.382][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-16 22:09:25.384][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:25.413][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:09:25.414][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-16 22:09:25.418][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:09:25.422][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-16 22:09:25.427][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 22:09:25.428][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 22:09:25.429][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-16 22:09:25.430][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-16 22:09:25.440][biodb::testThat]
biodb.INFO [2024-10-16 22:09:25.441][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-16 22:09:25.441][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:25.442][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:25.446][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-10-16 22:09:25.448][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:25.452][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 22:09:25.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:25.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:25.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.513][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:25.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:25.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.517][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:25.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:25.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:25.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:25.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.548][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:25.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.553][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.557][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.561][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:25.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.565][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:25.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.573][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.584][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:25.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.588][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 22:09:25.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.600][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:25.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.680][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.691][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:25.717][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-16 22:09:25.720][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:25.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:25.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.723][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:25.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:25.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.727][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:25.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:25.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.731][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:25.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:25.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.764][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.796][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.800][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:25.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.833][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.834][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.837][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.875][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.877][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.880][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.923][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.931][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.932][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.934][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:25.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.946][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.950][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.957][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.960][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.961][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.983][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.984][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.985][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.997][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:25.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:25.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.001][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.004][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.008][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.009][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.011][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.012][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.022][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.023][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.025][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.029][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:26.030][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:26.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.032][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.036][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:26.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:26.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.039][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.043][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.044][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.046][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.051][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.052][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.053][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.057][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.058][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.060][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:26.067][biodb::testThat]
biodb.INFO [2024-10-16 22:09:26.067][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-16 22:09:26.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:26.069][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:26.082][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-10-16 22:09:26.089][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:26.094][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-10-16 22:09:26.095][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:26.096][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-10-16 22:09:26.097][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:26.120][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:26.121][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 22:09:26.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:26.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:26.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:26.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:26.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:26.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:26.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:26.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.157][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:26.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:26.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.161][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:26.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:26.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.164][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.168][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:26.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:26.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:26.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.176][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:26.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:26.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.180][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:26.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.184][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:26.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.187][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:26.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:26.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:26.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:26.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.203][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:26.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.207][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 22:09:26.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.218][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:26.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.248][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:26.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:26.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.254][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:26.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:26.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.266][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:26.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:26.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:26.307][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-16 22:09:26.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-16 22:09:26.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-16 22:09:26.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-16 22:09:26.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-16 22:09:26.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-16 22:09:26.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-16 22:09:26.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:26.337][biodb::testThat]
biodb.INFO [2024-10-16 22:09:26.339][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-16 22:09:26.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:26.340][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:26.343][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.344][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.346][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:26.347][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-10-16 22:09:26.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:26.390][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-16 22:09:26.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-16 22:09:26.415][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:26.417][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:26.418][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-10-16 22:09:26.903][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-10-16 22:09:27.324][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:27.328][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-10-16 22:09:27.353][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-10-16 22:09:27.357][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-10-16 22:09:27.374][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:27.375][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:27.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.378][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:27.383][biodb::testThat]
biodb.INFO [2024-10-16 22:09:27.384][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-16 22:09:27.385][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:27.386][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:27.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:27.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:27.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:27.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:27.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:27.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:27.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:27.531][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-16 22:09:27.534][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:27.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-16 22:09:27.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:27.552][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-10-16 22:09:27.574][biodb::testThat]
biodb.INFO [2024-10-16 22:09:27.575][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-16 22:09:27.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:27.577][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:27.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.600][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.604][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:27.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:27.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.608][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:27.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:27.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.652][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.657][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:27.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.661][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:27.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:27.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:27.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:27.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:27.674][biodb::testThat]
biodb.INFO [2024-10-16 22:09:27.675][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-16 22:09:27.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:27.677][biodb::testThat]
biodb.INFO [2024-10-16 22:09:27.684][biodb::testThat]
biodb.INFO [2024-10-16 22:09:27.685][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-16 22:09:27.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:27.687][biodb::testThat]
biodb.INFO [2024-10-16 22:09:27.694][biodb::testThat]
biodb.INFO [2024-10-16 22:09:27.695][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-16 22:09:27.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:27.697][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:27.700][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-10-16 22:09:28.209][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-10-16 22:09:28.542][biodb::testThat]
biodb.INFO [2024-10-16 22:09:28.544][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-16 22:09:28.545][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:28.546][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:28.552][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:28.553][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:28.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.555][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.556][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.557][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.559][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:28.561][biodb::testThat]
biodb.INFO [2024-10-16 22:09:28.562][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-16 22:09:28.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:28.564][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:28.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:28.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:28.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:28.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:28.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:28.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:28.683][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-16 22:09:28.687][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:28.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-16 22:09:28.690][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:28.691][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-10-16 22:09:28.756][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-16 22:09:28.760][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:28.761][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-16 22:09:28.763][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:28.764][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-10-16 22:09:28.786][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:28.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:28.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:28.833][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-10-16 22:09:28.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:28.855][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:28.872][private$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[2024-10-16 22:09:29.623][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[2024-10-16 22:09:40.190][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:40.193][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-10-16 22:09:40.202][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-10-16 22:09:41.136][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-10-16 22:09:41.139][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:41.140][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:41.143][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-10-16 22:09:41.533][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-10-16 22:09:41.919][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:41.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-10-16 22:09:41.925][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-10-16 22:09:41.943][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-10-16 22:09:41.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:41.948][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:09:41.949][rule$waitAsNeeded] Wait 0.192795 second(s).
biodb.TRACE[2024-10-16 22:09:42.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-10-16 22:09:42.530][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-10-16 22:09:42.951][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:42.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-10-16 22:09:42.958][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-10-16 22:09:42.974][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:42.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:42.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:42.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:42.986][biodb::testThat]
biodb.INFO [2024-10-16 22:09:42.987][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-16 22:09:42.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:42.989][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:42.993][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:42.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:42.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:42.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:42.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:42.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:43.035][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-16 22:09:43.038][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:43.040][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:09:43.041][rule$waitAsNeeded] Wait 0.102524 second(s).
biodb.TRACE[2024-10-16 22:09:43.145][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-10-16 22:09:43.679][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-10-16 22:09:56.471][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:56.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-10-16 22:09:56.485][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-10-16 22:09:57.347][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-10-16 22:09:57.393][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-16 22:09:57.395][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-10-16 22:09:57.396][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-16 22:09:57.397][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:57.398][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:57.399][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 22:09:57.401][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:57.401][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:57.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:57.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:57.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:57.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.440][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-10-16 22:09:57.445][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:57.446][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:57.449][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-10-16 22:09:57.981][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-10-16 22:09:58.338][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:58.345][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-10-16 22:09:58.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-10-16 22:09:58.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:58.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.363][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-10-16 22:09:58.366][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:58.367][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:09:58.369][rule$waitAsNeeded] Wait 0.0796111 second(s).
biodb.TRACE[2024-10-16 22:09:58.450][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-10-16 22:09:58.975][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-10-16 22:09:59.567][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:59.572][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-10-16 22:09:59.580][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-10-16 22:09:59.587][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-10-16 22:09:59.591][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:59.594][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-16 22:09:59.597][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 22:09:59.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:59.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:59.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:59.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.678][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:59.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:59.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:59.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.686][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.690][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.703][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:59.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:59.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.707][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:59.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:59.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:59.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:59.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.716][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:59.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.729][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:59.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.733][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 22:09:59.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.741][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.745][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:59.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.749][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.760][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:59.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:59.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:59.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:59.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:59.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.809][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:59.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:09:59.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.813][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:59.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:59.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.817][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.821][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:09:59.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.825][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.828][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:09:59.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.832][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:59.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:59.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.836][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:09:59.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:59.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:59.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:59.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:59.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:59.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.855][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:59.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.858][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 22:09:59.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:59.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.869][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:09:59.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:59.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.873][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.877][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.884][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:59.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:59.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:59.922][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-10-16 22:09:59.932][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:09:59.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:59.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:59.953][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.957][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.961][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:09:59.962][private$selectFields]
biodb.TRACE[2024-10-16 22:09:59.963][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:59.964][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:59.965][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:09:59.966][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.967][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.969][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.970][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.972][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.974][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.974][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:09:59.975][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:09:59.976][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.977][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.979][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.980][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:09:59.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:59.989][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:09:59.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:59.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.001][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-16 22:10:00.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:00.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:00.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:00.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:00.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:00.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:00.011][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.TRACE[2024-10-16 22:10:00.012][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.015][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.019][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.020][private$selectFields]
biodb.TRACE[2024-10-16 22:10:00.021][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:00.022][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:00.023][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.023][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.024][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.026][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.027][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.028][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.030][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.031][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.032][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.033][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.034][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.035][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.036][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:00.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.041][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.045][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.049][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-16 22:10:00.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:00.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:00.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:00.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:00.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:00.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:00.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:00.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.067][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.068][private$selectFields]
biodb.TRACE[2024-10-16 22:10:00.069][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:00.070][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:00.071][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.071][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.072][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.074][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.075][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.076][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.078][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.079][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.080][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:00.091][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.092][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.094][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.095][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:00.096][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.099][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:00.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.107][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-16 22:10:00.108][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:10:00.109][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:10:00.117][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:10:00.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:10:00.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:10:00.124][biodb::testThat]
biodb.INFO [2024-10-16 22:10:00.125][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-16 22:10:00.126][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:00.126][biodb::testThat]
biodb.TRACE[2024-10-16 22:10:00.129][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:10:00.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:10:00.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:10:00.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:10:00.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:00.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:00.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:00.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:10:00.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:00.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:00.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:00.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:00.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:00.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:00.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:00.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-10-16 22:10:00.226][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:00.227][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:00.229][private$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[2024-10-16 22:10:00.747][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[2024-10-16 22:10:11.807][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:11.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-10-16 22:10:11.820][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-10-16 22:10:12.909][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:10:12.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:12.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:12.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:12.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:12.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:12.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:12.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:12.953][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:12.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:12.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:12.980][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:12.981][private$selectFields]
biodb.TRACE[2024-10-16 22:10:12.982][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:12.983][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:12.984][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:12.985][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.986][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:12.988][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:12.989][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.990][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:12.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:12.992][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:12.993][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.003][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.004][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.005][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.007][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.008][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:13.009][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.021][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-16 22:10:13.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:13.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:13.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:13.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:13.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:13.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:13.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.036][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.040][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.041][private$selectFields]
biodb.TRACE[2024-10-16 22:10:13.041][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:13.042][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:13.043][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.044][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.045][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.047][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.048][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.049][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.051][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.052][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.053][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.054][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.055][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.057][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.058][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:13.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.067][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.071][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-16 22:10:13.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:13.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:13.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:13.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:13.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:13.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:13.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:13.085][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.094][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.095][private$selectFields]
biodb.TRACE[2024-10-16 22:10:13.096][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:13.097][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:13.098][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.100][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.101][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.103][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.104][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.106][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.108][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.109][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.110][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:13.112][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.113][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.115][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.116][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:13.118][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.123][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.128][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:13.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.134][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-16 22:10:13.135][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:10:13.136][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:10:13.146][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:10:13.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:10:13.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:10:13.155][biodb::testThat]
biodb.INFO [2024-10-16 22:10:13.156][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-16 22:10:13.157][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:13.158][biodb::testThat]
biodb.TRACE[2024-10-16 22:10:13.161][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:10:13.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:10:13.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:10:13.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:10:13.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:13.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:13.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:13.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:10:13.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:13.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:13.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:13.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:13.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:13.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:13.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:13.209][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-16 22:10:13.213][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:10:13.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-10-16 22:10:13.216][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:10:13.267][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-10-16 22:10:14.346][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:10:14.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:14.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:14.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:14.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:14.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:14.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:14.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:14.357][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.361][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.365][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.366][private$selectFields]
biodb.TRACE[2024-10-16 22:10:14.366][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:14.367][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:14.368][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.369][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.370][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.372][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.373][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.374][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.376][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.377][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.378][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.379][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.380][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.381][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.382][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:14.383][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.387][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.391][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.395][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-16 22:10:14.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:14.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:14.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:14.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:14.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:14.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:14.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:14.405][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.409][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.413][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.413][private$selectFields]
biodb.TRACE[2024-10-16 22:10:14.414][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:14.415][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:14.416][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.417][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.418][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.420][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.421][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.422][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.424][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.425][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.426][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.426][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.427][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.429][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.430][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:14.431][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.435][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.439][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.443][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-16 22:10:14.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:14.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:14.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:14.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:14.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:14.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:14.452][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.TRACE[2024-10-16 22:10:14.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.457][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.461][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.462][private$selectFields]
biodb.TRACE[2024-10-16 22:10:14.463][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:10:14.464][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:10:14.465][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.466][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.467][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.468][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.469][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.470][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.472][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.473][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.474][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:10:14.475][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.476][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.478][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.479][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-16 22:10:14.480][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.484][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:14.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:14.493][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-16 22:10:14.494][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:10:14.495][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:10:14.512][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:10:14.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:10:14.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:14.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:10:14.519][biodb::testThat]
biodb.INFO [2024-10-16 22:10:14.520][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-16 22:10:14.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:14.522][biodb::testThat]
biodb.DEBUG[2024-10-16 22:10:14.524][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-16 22:10:14.525][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:10:14.527][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-16 22:10:14.528][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:10:14.529][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:10:14.530][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:10:14.531][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 22:10:14.532][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:10:14.533][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:10:14.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:14.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:14.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:14.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:14.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:14.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:14.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:14.558][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-10-16 22:10:14.561][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:14.562][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:14.563][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:14.914][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:14.916][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:14.917][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:14.919][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:15.341][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:15.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:15.346][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:15.349][rule$waitAsNeeded] Wait 0.214275 second(s).
biodb.TRACE[2024-10-16 22:10:15.566][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:15.913][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:15.915][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:15.916][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:15.917][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:16.393][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:16.394][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:16.395][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:16.396][rule$waitAsNeeded] Wait 0.16956 second(s).
biodb.TRACE[2024-10-16 22:10:16.568][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:16.912][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:16.913][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:16.915][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:16.916][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:17.392][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:17.393][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:17.394][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:17.395][rule$waitAsNeeded] Wait 0.171884 second(s).
biodb.TRACE[2024-10-16 22:10:17.569][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:17.917][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:17.919][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:17.921][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:17.923][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:18.440][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:18.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:18.443][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:18.446][rule$waitAsNeeded] Wait 0.123466 second(s).
biodb.TRACE[2024-10-16 22:10:18.572][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:19.444][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:19.447][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:19.450][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:19.452][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:19.973][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:19.976][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:19.978][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:19.981][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:20.369][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:20.372][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:20.374][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:20.377][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:20.902][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:20.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:20.907][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:20.910][rule$waitAsNeeded] Wait 0.0716412 second(s).
biodb.TRACE[2024-10-16 22:10:20.985][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:21.382][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:21.384][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:21.385][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:21.387][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:21.864][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:21.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:21.866][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:21.867][rule$waitAsNeeded] Wait 0.116456 second(s).
biodb.TRACE[2024-10-16 22:10:21.986][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:22.384][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:22.386][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:22.389][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:22.391][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:22.912][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:22.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:22.916][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:22.918][rule$waitAsNeeded] Wait 0.0674219 second(s).
biodb.TRACE[2024-10-16 22:10:22.988][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:23.378][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:23.381][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:23.384][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:23.387][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:23.908][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:23.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:23.910][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:23.912][rule$waitAsNeeded] Wait 0.0756881 second(s).
biodb.TRACE[2024-10-16 22:10:23.989][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-16 22:10:24.336][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:24.337][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:24.339][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:24.340][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-16 22:10:24.839][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-10-16 22:10:24.842][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-10-16 22:10:24.843][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:10:24.845][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:10:24.846][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 22:10:24.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:24.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:24.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:24.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:24.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:24.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:24.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:24.860][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:24.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:24.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:24.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:24.865][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:24.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:24.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:24.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:24.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:24.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:24.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:24.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:24.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:24.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:24.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:24.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:24.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:24.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:24.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:24.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:25.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:25.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:25.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:25.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:25.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:25.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:25.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:25.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:25.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:10:25.122][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-10-16 22:10:25.123][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-16 22:10:25.129][biodb::testThat]
biodb.INFO [2024-10-16 22:10:25.130][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-16 22:10:25.131][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:25.132][biodb::testThat]
biodb.DEBUG[2024-10-16 22:10:25.138][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-10-16 22:10:25.139][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-10-16 22:10:25.140][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-16 22:10:25.141][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-10-16 22:10:25.142][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-16 22:10:25.143][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:10:25.144][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:10:25.145][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 22:10:25.146][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:10:25.147][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:10:25.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:25.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:25.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:25.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:25.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:25.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:25.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:25.160][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-10-16 22:10:25.162][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:25.163][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:25.164][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:25.515][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:25.516][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:25.517][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:25.518][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:26.003][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:26.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:26.006][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:26.008][rule$waitAsNeeded] Wait 0.156068 second(s).
biodb.TRACE[2024-10-16 22:10:26.167][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:26.784][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:26.786][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:26.787][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:26.788][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:27.270][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:27.272][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:27.274][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:27.276][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:27.654][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:27.656][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:27.658][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:27.660][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:28.180][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:28.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:28.185][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:28.187][rule$waitAsNeeded] Wait 0.0890527 second(s).
biodb.TRACE[2024-10-16 22:10:28.279][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:28.679][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:28.681][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:28.684][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:28.686][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:29.207][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:29.209][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:29.211][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:29.213][rule$waitAsNeeded] Wait 0.0661032 second(s).
biodb.TRACE[2024-10-16 22:10:29.281][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:29.833][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:29.834][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:29.836][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:29.837][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:30.335][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:30.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:30.339][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:30.342][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:30.727][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:30.729][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:30.731][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:30.732][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:31.246][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:31.247][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:31.248][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:31.249][rule$waitAsNeeded] Wait 0.0926809 second(s).
biodb.TRACE[2024-10-16 22:10:31.343][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:31.689][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:31.690][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:31.691][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:31.692][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:32.173][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:32.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:32.177][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:32.180][rule$waitAsNeeded] Wait 0.163024 second(s).
biodb.TRACE[2024-10-16 22:10:32.346][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:32.739][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:32.741][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:32.743][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:32.746][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:33.225][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:33.226][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:33.227][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:33.228][rule$waitAsNeeded] Wait 0.116936 second(s).
biodb.TRACE[2024-10-16 22:10:33.347][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:33.699][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:33.701][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:33.702][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:33.703][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:34.182][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:34.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:34.184][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:34.186][rule$waitAsNeeded] Wait 0.160763 second(s).
biodb.TRACE[2024-10-16 22:10:34.349][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-16 22:10:34.742][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-16 22:10:34.745][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-16 22:10:34.748][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-16 22:10:34.751][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-16 22:10:35.171][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-16 22:10:35.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:35.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:35.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:35.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:35.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:35.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:35.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:35.204][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-10-16 22:10:35.211][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:35.214][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:35.216][rule$waitAsNeeded] Wait 0.131918 second(s).
biodb.TRACE[2024-10-16 22:10:35.351][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-10-16 22:10:35.902][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2024-10-16 22:10:36.285][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:36.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2024-10-16 22:10:36.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2024-10-16 22:10:36.302][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-10-16 22:10:36.306][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:10:36.309][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-16 22:10:36.312][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 22:10:36.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:36.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:36.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:36.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:36.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:36.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:36.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:36.338][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:10:36.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:36.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:36.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:36.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:36.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:36.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:36.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:10:36.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:10:36.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:10:36.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:10:36.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.388][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:10:36.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:10:36.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.393][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:10:36.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:10:36.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.397][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:36.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:36.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.401][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:36.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:36.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:10:36.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:10:36.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.409][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:10:36.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:10:36.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:10:36.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:10:36.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:10:36.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:10:36.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:10:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:36.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.426][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:10:36.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:36.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.430][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:10:36.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:10:36.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.434][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:10:36.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:10:36.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.447][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:10:36.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.451][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 22:10:36.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.464][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:10:36.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:36.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:36.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.488][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.492][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.500][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:10:36.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:36.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:36.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:36.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:36.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:10:36.563][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2024-10-16 22:10:36.582][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-16 22:10:36.583][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-16 22:10:36.596][biodb::testThat]
biodb.INFO [2024-10-16 22:10:36.597][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-16 22:10:36.598][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:36.599][biodb::testThat]
biodb.INFO [2024-10-16 22:10:36.620][biodb::testThat]
biodb.INFO [2024-10-16 22:10:36.622][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-16 22:10:36.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:36.624][biodb::testThat]
biodb.INFO [2024-10-16 22:10:36.631][biodb::testThat]
biodb.INFO [2024-10-16 22:10:36.632][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-16 22:10:36.633][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:36.634][biodb::testThat]
biodb.DEBUG[2024-10-16 22:10:36.637][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-16 22:10:36.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:36.641][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:36.643][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-10-16 22:10:37.435][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-10-16 22:10:49.031][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:49.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-10-16 22:10:49.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-10-16 22:10:49.893][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:49.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:49.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:49.896][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:49.897][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:49.898][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:49.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:49.900][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:10:49.901][biodb::testThat]
biodb.INFO [2024-10-16 22:10:49.902][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-16 22:10:49.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:49.904][biodb::testThat]
biodb.ERROR[2024-10-16 22:10:49.916][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-16 22:10:49.932][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-16 22:10:49.944][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:10:49.945][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-16 22:10:49.946][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-16 22:10:49.947][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:10:49.948][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:49.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:49.950][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:49.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:49.952][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:49.953][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.INFO [2024-10-16 22:10:49.963][biodb::testContext]
biodb.INFO [2024-10-16 22:10:49.964][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:10:49.965][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-10-16 22:10:49.966][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:10:49.967][biodb::testContext]
biodb.INFO [2024-10-16 22:10:49.969][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:10:49.971][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:10:49.975][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:10:49.976][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:10:49.977][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:10:49.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:49.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:49.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:49.981][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:10:49.982][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:10:49.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:49.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:49.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:49.986][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:10:49.987][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:10:49.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:49.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:49.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:49.990][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:10:49.991][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:10:49.992][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:10:49.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:49.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:49.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:49.996][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:10:49.997][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:10:49.998][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:10:49.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.001][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:10:50.002][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:10:50.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.005][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[2024-10-16 22:10:50.006][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:10:50.007][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:10:50.008][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:10:50.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.011][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:10:50.012][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:10:50.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.016][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:10:50.017][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:10:50.018][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:10:50.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.022][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:10:50.023][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:10:50.023][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:10:50.024][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:10:50.025][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:10:50.026][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:10:50.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.030][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:10:50.031][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:10:50.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.034][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:10:50.035][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:10:50.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.039][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:10:50.040][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:10:50.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.043][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:10:50.044][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:10:50.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.047][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[2024-10-16 22:10:50.048][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:10:50.049][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:10:50.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.052][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:10:50.053][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:10:50.056][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:10:50.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.060][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:10:50.061][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:10:50.061][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:10:50.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.065][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:10:50.067][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.068][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:10:50.069][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.070][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:10:50.071][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.073][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.075][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:10:50.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:10:50.077][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.078][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:10:50.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:10:50.080][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.081][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.081][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:10:50.081][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:10:50.081][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:10:50.081][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:10:50.081][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:10:50.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:10:50.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:10:50.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.088][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.089][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.090][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:10:50.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:10:50.092][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.093][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.094][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:10:50.096][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.096][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:10:50.097][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.098][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:10:50.099][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.100][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.101][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.102][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.103][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:10:50.104][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:10:50.105][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.106][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:10:50.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:10:50.108][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.109][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.110][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:10:50.110][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:10:50.110][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:10:50.110][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:10:50.110][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:10:50.111][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:10:50.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.114][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:10:50.115][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.118][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:10:50.119][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:10:50.120][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.121][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.122][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:10:50.124][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.125][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:10:50.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:10:50.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.132][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:10:50.132][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:10:50.133][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.134][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:10:50.135][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:10:50.136][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.137][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.138][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.139][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:10:50.140][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.141][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.142][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:10:50.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.144][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.145][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.146][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:10:50.147][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:10:50.148][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.149][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.150][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:10:50.152][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.153][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:10:50.154][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.155][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:10:50.156][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.157][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.158][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.159][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.160][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:10:50.161][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:10:50.162][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.163][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:10:50.164][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:10:50.165][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.166][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.167][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.168][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:10:50.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.170][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.171][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:10:50.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.174][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.175][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.176][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:10:50.177][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:10:50.178][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.179][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.180][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:10:50.181][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.182][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[2024-10-16 22:10:50.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.204][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[2024-10-16 22:10:50.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.209][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[2024-10-16 22:10:50.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.223][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[2024-10-16 22:10:50.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.231][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[2024-10-16 22:10:50.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.269][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:10:50.270][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:10:50.272][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:10:50.273][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:10:50.274][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:10:50.276][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:10:50.277][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:10:50.278][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:10:50.279][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:10:50.281][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:10:50.282][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:10:50.283][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:10:50.284][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:10:50.286][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:10:50.287][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:10:50.288][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:10:50.289][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:10:50.291][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:10:50.292][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:10:50.293][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:10:50.294][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:10:50.296][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:10:50.297][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:10:50.298][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:10:50.299][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:10:50.301][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:10:50.302][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:10:50.303][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:10:50.304][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:10:50.306][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:10:50.307][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:10:50.308][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:10:50.310][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:10:50.311][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:10:50.312][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:10:50.313][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:10:50.315][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:10:50.316][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:10:50.317][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:10:50.318][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:10:50.320][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:10:50.321][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:10:50.322][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:10:50.323][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:10:50.325][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:10:50.326][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:10:50.327][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:10:50.329][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:10:50.330][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:10:50.331][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:10:50.332][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:10:50.334][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:10:50.335][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:10:50.336][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:10:50.337][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:10:50.339][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:10:50.340][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:10:50.341][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:10:50.343][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:10:50.344][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:10:50.345][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:10:50.346][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:10:50.348][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:10:50.349][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:10:50.350][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:10:50.351][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:10:50.353][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:10:50.354][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:10:50.355][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:10:50.357][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:10:50.358][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:10:50.359][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:10:50.360][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:10:50.362][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:10:50.363][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:10:50.364][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:10:50.366][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:10:50.367][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:10:50.368][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:10:50.370][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:10:50.371][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:10:50.372][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:10:50.374][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:10:50.375][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:10:50.377][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:10:50.378][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:10:50.378][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.380][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.474][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.DEBUG[2024-10-16 22:10:50.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:10:50.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:50.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:50.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:50.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:50.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:50.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:10:50.482][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-16 22:10:50.483][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:10:50.485][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.486][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.487][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.488][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:10:50.488][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.489][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.490][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.491][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.492][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:10:50.493][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:10:50.494][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.495][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-16 22:10:50.496][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-16 22:10:50.497][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-16 22:10:50.498][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:10:50.499][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:10:50.499][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:10:50.500][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:10:50.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.502][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:10:50.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:10:50.504][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:10:50.505][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:10:50.506][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 22:10:50.506][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-16 22:10:50.507][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:10:50.508][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:10:50.508][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:50.509][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:10:50.511][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-16 22:10:50.512][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:10:50.515][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:10:50.516][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-16 22:10:50.517][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:10:50.518][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-16 22:10:50.519][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 22:10:50.520][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 22:10:50.521][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-16 22:10:50.522][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-16 22:10:50.524][biodb::testThat]
biodb.INFO [2024-10-16 22:10:50.525][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-10-16 22:10:50.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:50.526][biodb::testThat]
biodb.DEBUG[2024-10-16 22:10:50.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-10-16 22:10:50.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:50.534][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:50.536][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-10-16 22:10:50.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-10-16 22:10:51.336][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:51.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-10-16 22:10:51.351][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-10-16 22:10:51.374][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-10-16 22:10:51.381][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:51.383][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:51.385][rule$waitAsNeeded] Wait 0.150665 second(s).
biodb.TRACE[2024-10-16 22:10:51.539][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-10-16 22:10:51.970][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-10-16 22:10:52.374][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:52.378][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-10-16 22:10:52.384][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-10-16 22:10:52.447][biodb::testThat]
biodb.INFO [2024-10-16 22:10:52.449][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-10-16 22:10:52.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:52.453][biodb::testThat]
biodb.INFO [2024-10-16 22:10:52.484][biodb::testThat]
biodb.INFO [2024-10-16 22:10:52.485][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-10-16 22:10:52.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:52.487][biodb::testThat]
biodb.DEBUG[2024-10-16 22:10:52.490][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-16 22:10:52.493][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:52.494][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:52.495][rule$waitAsNeeded] Wait 0.0427639 second(s).
biodb.TRACE[2024-10-16 22:10:52.540][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-10-16 22:10:52.884][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-10-16 22:10:53.542][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:53.545][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-10-16 22:10:53.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-10-16 22:10:53.554][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-16 22:10:53.557][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:10:53.558][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-10-16 22:10:53.560][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:10:53.561][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-10-16 22:10:53.567][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-10-16 22:10:53.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:53.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:53.573][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-10-16 22:10:53.923][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[2024-10-16 22:10:54.283][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:54.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-10-16 22:10:54.301][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-10-16 22:10:54.320][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-10-16 22:10:54.327][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:54.329][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-16 22:10:54.331][rule$waitAsNeeded] Wait 0.241391 second(s).
biodb.TRACE[2024-10-16 22:10:54.576][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-10-16 22:10:55.097][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-10-16 22:10:57.725][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:57.728][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-10-16 22:10:57.732][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-10-16 22:10:57.853][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-10-16 22:10:57.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:57.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:57.860][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-10-16 22:10:58.382][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-10-16 22:11:01.471][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:11:01.474][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-10-16 22:11:01.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-10-16 22:11:01.599][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:11:01.601][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-16 22:11:01.602][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-16 22:11:01.603][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:11:01.604][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:01.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:01.606][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.608][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:11:01.613][biodb::testContext]
biodb.INFO [2024-10-16 22:11:01.613][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:11:01.614][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-10-16 22:11:01.615][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:11:01.616][biodb::testContext]
biodb.INFO [2024-10-16 22:11:01.619][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:11:01.620][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:11:01.624][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:11:01.625][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:11:01.626][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:11:01.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.630][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:11:01.631][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:11:01.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.635][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:11:01.636][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:11:01.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.640][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:11:01.641][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:11:01.642][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:11:01.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.645][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:11:01.646][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:11:01.647][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:11:01.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.651][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:11:01.652][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:11:01.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.656][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:11:01.657][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:11:01.658][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:11:01.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.661][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:11:01.662][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:11:01.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.666][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:11:01.667][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:11:01.668][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:11:01.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.672][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:11:01.673][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:11:01.674][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:11:01.675][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:11:01.676][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:11:01.677][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:11:01.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.680][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:11:01.681][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:11:01.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.685][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:11:01.686][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:11:01.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.690][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:11:01.691][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:11:01.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.695][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:11:01.696][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:11:01.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.699][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:11:01.700][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:11:01.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.704][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:11:01.705][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:11:01.708][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:11:01.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.712][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:11:01.713][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:11:01.714][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:11:01.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.717][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[2024-10-16 22:11:01.772][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:11:01.774][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.775][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:11:01.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.777][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:11:01.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.779][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.780][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.781][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.782][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:11:01.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:11:01.784][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.785][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:11:01.786][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:11:01.787][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.788][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.789][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:11:01.789][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:11:01.789][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:11:01.789][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:11:01.789][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:11:01.790][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:11:01.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.793][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:11:01.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.797][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:11:01.799][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:11:01.800][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.801][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.802][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:11:01.804][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.805][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:11:01.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:11:01.808][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.809][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.810][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.811][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.812][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:11:01.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:11:01.814][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.815][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:11:01.816][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:11:01.817][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.818][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.819][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:11:01.819][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:11:01.819][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:11:01.819][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:11:01.819][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:11:01.820][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:11:01.821][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.823][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:11:01.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.826][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.827][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.828][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:11:01.828][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:11:01.829][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.830][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.832][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:11:01.833][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.834][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:11:01.835][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:11:01.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.838][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.839][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.840][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.841][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:11:01.842][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:11:01.843][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.844][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:11:01.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:11:01.846][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.847][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.848][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:11:01.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:11:01.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.856][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.857][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:11:01.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:11:01.859][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.860][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.861][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:11:01.863][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.864][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:11:01.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.866][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:11:01.867][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.870][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.871][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:11:01.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:11:01.873][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.874][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:11:01.875][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:11:01.876][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.877][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:01.878][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.879][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:11:01.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:11:01.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:01.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:01.884][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:11:01.885][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.886][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:11:01.887][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:11:01.888][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:01.889][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:01.891][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:11:01.892][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.902][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[2024-10-16 22:11:01.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:01.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:01.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:01.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:01.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:01.970][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:11:01.971][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:11:01.973][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:11:01.974][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:11:01.975][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:11:01.977][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:11:01.978][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:11:01.980][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:11:01.981][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:11:01.982][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:11:01.984][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:11:01.985][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:11:01.986][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:11:01.988][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:11:01.989][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:11:01.990][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:11:01.992][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:11:01.993][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:11:01.995][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:11:01.996][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:11:01.997][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:11:01.999][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:11:02.000][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:11:02.002][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:11:02.003][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:11:02.004][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:11:02.006][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:11:02.007][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:11:02.008][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:11:02.010][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:11:02.011][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:11:02.013][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:11:02.014][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:11:02.015][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:11:02.017][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:11:02.018][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:11:02.020][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:11:02.021][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:11:02.022][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:11:02.024][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:11:02.025][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:11:02.027][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:11:02.028][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:11:02.029][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:11:02.031][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:11:02.032][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:11:02.034][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:11:02.035][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:11:02.036][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:11:02.038][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:11:02.039][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:11:02.041][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:11:02.042][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:11:02.043][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:11:02.045][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:11:02.046][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:11:02.048][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:11:02.049][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:11:02.050][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:11:02.052][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:11:02.053][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:11:02.054][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:11:02.056][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:11:02.057][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:11:02.059][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:11:02.060][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:11:02.062][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:11:02.063][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:11:02.065][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:11:02.066][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:11:02.067][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:11:02.069][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:11:02.070][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:11:02.072][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:11:02.073][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:11:02.075][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:11:02.076][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:11:02.077][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:11:02.079][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:11:02.080][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:11:02.082][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:11:02.083][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:11:02.084][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:11:02.086][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:11:02.088][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:11:02.089][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:11:02.090][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.092][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.182][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[2024-10-16 22:11:02.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:11:02.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:02.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:02.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:02.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:02.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:02.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:11:02.212][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-16 22:11:02.213][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:11:02.215][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:02.216][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:11:02.217][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:02.218][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:11:02.219][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:02.220][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:11:02.221][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:02.222][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:11:02.223][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:11:02.223][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:11:02.224][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:02.225][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-16 22:11:02.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-16 22:11:02.227][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-16 22:11:02.228][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:11:02.229][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:11:02.229][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:11:02.230][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:11:02.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:02.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:02.233][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:11:02.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:11:02.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:11:02.235][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:11:02.236][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-16 22:11:02.236][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-16 22:11:02.237][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:11:02.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:11:02.239][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:11:02.240][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:11:02.241][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-16 22:11:02.242][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:11:02.247][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:11:02.248][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-16 22:11:02.249][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-16 22:11:02.250][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-16 22:11:02.251][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 22:11:02.252][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-16 22:11:02.254][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-16 22:11:02.255][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-16 22:11:02.256][biodb::testThat]
biodb.INFO [2024-10-16 22:11:02.257][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-10-16 22:11:02.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:11:02.259][biodb::testThat]
biodb.DEBUG[2024-10-16 22:11:02.262][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-16 22:11:02.267][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:11:02.268][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-10-16 22:11:02.269][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:11:02.317][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-10-16 22:11:03.438][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-10-16 22:11:03.439][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-16 22:11:03.441][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-10-16 22:11:03.442][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-10-16 22:11:03.443][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-10-16 22:11:03.444][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:11:03.445][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-16 22:11:03.446][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-16 22:11:03.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:11:03.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:03.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:03.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:03.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:03.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:03.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:11:03.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.477][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:11:03.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:11:03.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.480][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:11:03.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:11:03.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.484][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.488][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.499][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:11:03.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.503][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:11:03.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.507][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.510][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.521][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:11:03.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.525][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 22:11:03.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.536][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:11:03.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.593][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.601][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:11:03.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:11:03.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:03.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:03.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:03.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:03.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:03.625][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.TRACE[2024-10-16 22:11:03.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.645][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:11:03.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-16 22:11:03.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:11:03.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:11:03.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.652][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.656][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.668][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:11:03.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.672][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-16 22:11:03.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.676][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.680][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.692][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:11:03.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.696][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-16 22:11:03.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.707][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-16 22:11:03.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.711][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.715][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.723][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:11:03.762][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-10-16 22:11:03.765][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:11:03.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:11:03.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:03.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:03.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:03.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:03.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:03.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:11:03.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:11:03.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:11:03.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:11:03.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:11:03.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:11:03.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:11:03.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:11:03.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:11:03.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.805][private$selectFields] Fields none
biodb.TRACE[2024-10-16 22:11:03.806][private$selectFields]
biodb.TRACE[2024-10-16 22:11:03.807][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-16 22:11:03.808][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:11:03.808][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:11:03.809][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.810][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.812][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.814][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.816][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.816][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.817][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.819][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.820][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.821][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.823][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.824][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.825][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.826][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.827][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.828][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.830][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.831][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.832][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.833][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.834][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.835][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.837][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.838][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.840][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.841][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.842][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.844][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.845][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.846][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.847][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.848][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.849][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.851][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.852][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.854][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.855][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.856][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.858][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.859][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.862][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.862][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.863][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.865][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.866][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:11:03.867][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:11:03.868][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.869][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.870][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.871][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.872][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.874][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.875][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.876][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.878][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.878][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.879][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.881][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.882][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.883][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.885][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.885][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.888][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.889][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.890][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.892][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.893][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.894][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.895][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.896][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-10-16 22:11:03.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:03.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:03.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:03.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.920][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.923][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.927][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:03.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.938][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:03.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:03.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.957][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.961][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:03.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:03.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:03.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:03.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.976][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.979][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.983][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:03.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:03.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:03.992][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-10-16 22:11:03.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:11:03.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:03.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:03.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:04.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:04.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:04.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:11:04.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:11:04.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:11:04.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.007][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:11:04.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:11:04.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.011][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:11:04.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:11:04.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.015][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:11:04.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:11:04.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.018][private$selectFields] Fields none
biodb.TRACE[2024-10-16 22:11:04.019][private$selectFields]
biodb.TRACE[2024-10-16 22:11:04.020][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-16 22:11:04.021][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:11:04.022][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:11:04.023][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:04.024][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:04.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.026][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.026][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.027][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.029][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.030][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.031][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.033][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.034][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.035][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.036][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.037][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.038][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.040][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.041][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:04.042][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:04.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.043][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.044][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:04.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:04.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.047][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.048][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.049][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.051][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.052][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:04.053][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:04.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.054][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.055][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.056][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.058][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.059][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.060][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.061][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.062][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.063][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.065][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.066][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.067][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.069][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.070][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:04.071][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:04.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.072][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.073][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:04.074][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:04.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.077][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.078][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.080][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.081][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:11:04.081][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-16 22:11:04.082][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:04.083][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:04.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.085][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.089][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.090][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.091][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.092][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.093][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.094][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.096][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.097][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.098][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.100][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.100][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:04.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:04.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.103][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.104][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:04.105][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:04.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.117][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.118][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.119][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.121][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.122][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-10-16 22:11:04.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:04.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:04.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:04.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:04.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:11:04.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:11:04.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:11:04.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.145][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.152][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-16 22:11:04.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.156][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.159][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-16 22:11:04.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:11:04.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:04.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:04.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.181][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:04.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:04.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.185][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:11:04.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:11:04.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:04.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:04.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:04.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:04.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:11:04.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:11:04.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.199][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.203][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.207][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-16 22:11:04.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:11:04.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:11:04.214][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-10-16 22:11:04.215][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:11:04.215][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-10-16 22:11:04.220][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:11:04.221][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-16 22:11:04.222][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-16 22:11:04.223][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:11:04.224][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:11:04.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:11:04.225][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:11:04.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:11:04.227][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:11:04.228][FUN] Functions in observer 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 
 23.113   2.179 101.398

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn0.9120.1162.951
LipidmapsStructureEntry0.1710.0010.172