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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on kjohnson3

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

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-10 08:53:39 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 08:57:22 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 223.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 2.338  0.699   6.169
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’
for details.

Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-06-10 08:54:52.908][biodb::testContext]
biodb.INFO [2024-06-10 08:54:52.913][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:52.915][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-10 08:54:52.919][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:52.921][biodb::testContext]
biodb.INFO [2024-06-10 08:54:52.931][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:52.935][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:52.946][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:52.949][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 08:54:52.950][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 08:54:52.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:52.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:52.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:52.956][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 08:54:52.981][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 08:54:52.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:52.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:52.985][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[2024-06-10 08:54:52.986][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 08:54:52.988][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 08:54:53.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.026][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 08:54:53.029][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 08:54:53.031][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 08:54:53.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.038][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 08:54:53.040][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 08:54:53.042][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 08:54:53.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.047][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 08:54:53.051][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 08:54:53.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.058][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 08:54:53.060][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 08:54:53.061][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 08:54:53.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.066][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 08:54:53.068][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 08:54:53.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.073][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 08:54:53.074][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 08:54:53.075][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 08:54:53.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.079][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:53.080][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 08:54:53.081][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 08:54:53.083][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 08:54:53.084][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 08:54:53.085][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 08:54:53.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.089][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 08:54:53.090][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 08:54:53.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.094][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 08:54:53.098][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 08:54:53.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.101][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 08:54:53.103][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 08:54:53.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.109][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 08:54:53.110][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 08:54:53.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.113][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 08:54:53.114][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 08:54:53.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.117][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:53.118][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 08:54:53.154][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 08:54:53.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.161][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 08:54:53.163][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 08:54:53.165][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 08:54:53.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.175][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 08:54:53.221][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.243][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 08:54:53.244][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.245][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:53.247][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.248][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.248][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.249][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.250][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:53.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:53.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.253][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 08:54:53.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:53.255][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.258][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:53.258][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:53.258][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:53.258][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:53.258][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:53.259][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:53.260][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:53.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.268][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:53.270][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:53.274][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.275][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.276][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 08:54:53.279][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.280][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:53.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.283][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:53.284][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.286][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.288][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.290][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:53.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:53.294][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.296][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 08:54:53.297][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:53.298][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.300][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.300][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:53.300][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:53.300][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:53.300][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:53.300][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:53.301][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:53.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.305][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:53.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.310][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.311][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.316][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:53.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:53.319][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.324][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.326][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 08:54:53.331][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.333][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 08:54:53.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.361][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:53.362][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.364][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.366][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:53.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:53.370][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.371][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 08:54:53.372][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:53.373][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.374][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.375][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.376][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:53.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:53.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.385][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.386][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.387][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:53.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:53.390][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.392][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.393][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 08:54:53.395][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.396][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:53.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.399][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:53.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.407][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:53.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:53.409][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.410][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 08:54:53.413][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:53.415][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.416][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.416][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.417][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:53.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:53.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.423][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.424][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:53.425][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:53.425][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.426][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.432][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:53.435][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.445][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[2024-06-10 08:54:53.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.457][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[2024-06-10 08:54:53.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.530][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 08:54:53.535][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 08:54:53.538][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 08:54:53.540][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 08:54:53.541][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:54:53.544][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 08:54:53.545][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:53.549][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:53.550][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 08:54:53.552][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 08:54:53.554][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:54:53.555][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 08:54:53.556][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:53.560][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:53.561][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 08:54:53.563][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:54:53.565][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 08:54:53.567][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 08:54:53.569][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:54:53.570][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 08:54:53.572][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 08:54:53.574][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 08:54:53.576][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 08:54:53.577][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 08:54:53.579][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 08:54:53.582][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 08:54:53.583][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 08:54:53.587][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 08:54:53.589][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 08:54:53.592][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 08:54:53.594][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 08:54:53.596][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 08:54:53.597][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 08:54:53.599][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 08:54:53.602][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 08:54:53.604][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 08:54:53.606][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 08:54:53.607][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 08:54:53.608][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 08:54:53.623][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 08:54:53.624][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 08:54:53.626][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 08:54:53.627][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 08:54:53.628][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 08:54:53.629][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 08:54:53.631][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 08:54:53.632][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 08:54:53.633][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 08:54:53.635][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 08:54:53.636][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 08:54:53.637][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 08:54:53.639][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 08:54:53.640][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 08:54:53.641][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 08:54:53.643][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 08:54:53.644][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 08:54:53.645][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 08:54:53.647][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 08:54:53.648][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 08:54:53.649][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 08:54:53.651][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 08:54:53.652][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 08:54:53.653][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 08:54:53.655][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 08:54:53.656][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 08:54:53.658][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 08:54:53.659][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:54:53.660][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:54:53.662][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 08:54:53.663][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 08:54:53.664][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 08:54:53.665][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 08:54:53.667][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 08:54:53.668][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 08:54:53.669][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 08:54:53.670][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 08:54:53.672][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 08:54:53.673][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 08:54:53.674][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 08:54:53.675][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 08:54:53.677][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 08:54:53.678][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 08:54:53.679][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 08:54:53.685][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 08:54:53.687][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:53.691][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:53.692][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.694][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.694][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[2024-06-10 08:54:53.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.703][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[2024-06-10 08:54:53.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.713][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[2024-06-10 08:54:53.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.738][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[2024-06-10 08:54:53.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:53.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:53.797][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:53.821][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:54:53.823][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.824][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.826][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:53.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.828][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.829][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.830][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.830][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:53.831][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:53.832][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.833][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-10 08:54:53.834][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-10 08:54:53.835][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-10 08:54:53.837][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:53.838][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:53.838][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:53.839][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:53.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.841][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:53.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:53.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:53.844][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:53.845][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-10 08:54:53.845][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-10 08:54:53.845][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:53.846][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:53.847][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:53.848][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:53.854][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-10 08:54:53.856][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:54:53.890][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:54:53.892][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-10 08:54:53.896][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:54:53.901][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-10 08:54:53.905][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-10 08:54:53.906][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-10 08:54:53.908][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-10 08:54:53.909][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-10 08:54:53.920][biodb::testThat]
biodb.INFO [2024-06-10 08:54:53.921][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-10 08:54:53.922][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:53.923][biodb::testThat]
biodb.TRACE[2024-06-10 08:54:53.931][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-10 08:54:53.934][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:54:53.939][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-10 08:54:53.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:53.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:53.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:53.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:53.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:53.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:53.986][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:54:54.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:54.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.035][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:54:54.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:54:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.043][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:54.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:54.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.047][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.117][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.130][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.136][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:54:54.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.145][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:54:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.152][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.162][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.178][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:54:54.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.184][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-10 08:54:54.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:54:54.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.301][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.307][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.315][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:54.435][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-10 08:54:54.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:54:54.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:54:54.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:54:54.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:54:54.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:54:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:54:54.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.458][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:54:54.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:54:54.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.507][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.545][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.548][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:54.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.581][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.584][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.641][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.643][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.645][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.668][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.688][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.690][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.694][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.717][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.738][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.740][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.743][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.746][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.794][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.795][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.799][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.840][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.850][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.852][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.857][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.878][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:54.880][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:54.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.893][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.894][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:54.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.897][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.906][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:54.907][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:54.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.909][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.918][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.920][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:54.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.928][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:54.949][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:54.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:54.961][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.963][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:54.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:54.966][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:54:54.982][biodb::testThat]
biodb.INFO [2024-06-10 08:54:54.985][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-10 08:54:54.986][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:54.987][biodb::testThat]
biodb.DEBUG[2024-06-10 08:54:55.011][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-10 08:54:55.022][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:54:55.030][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-10 08:54:55.033][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:55.035][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-10 08:54:55.037][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:54:55.078][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:54:55.080][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-10 08:54:55.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:55.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:55.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:55.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:55.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:55.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:55.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:54:55.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:55.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:55.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:55.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:55.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.140][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:54:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:54:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:55.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:55.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.151][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:55.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:54:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:54:55.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:54:55.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:55.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.180][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:54:55.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:55.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:55.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:55.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:55.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:55.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.228][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:54:55.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.235][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-10 08:54:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.250][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:54:55.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:55.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:55.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.280][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:55.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:55.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.287][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:55.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:54:55.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:55.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:55.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:55.310][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-10 08:54:55.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-10 08:54:55.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-10 08:54:55.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-10 08:54:55.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-10 08:54:55.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-10 08:54:55.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-10 08:54:55.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:54:55.333][biodb::testThat]
biodb.INFO [2024-06-10 08:54:55.335][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-10 08:54:55.336][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:55.336][biodb::testThat]
biodb.TRACE[2024-06-10 08:54:55.340][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.342][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.344][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:55.346][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-10 08:54:55.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:55.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:55.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:55.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:55.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:55.404][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-10 08:54:55.410][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[2024-06-10 08:54:55.433][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:55.435][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:55.437][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-10 08:54:56.409][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-10 08:54:57.073][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:57.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-10 08:54:57.146][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-10 08:54:57.152][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-10 08:54:57.180][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:57.182][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:57.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.185][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:54:57.195][biodb::testThat]
biodb.INFO [2024-06-10 08:54:57.196][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-10 08:54:57.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:57.198][biodb::testThat]
biodb.TRACE[2024-06-10 08:54:57.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:57.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:57.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:57.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:57.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:57.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:57.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:57.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-10 08:54:57.424][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:57.447][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-10 08:54:57.448][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:57.450][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-10 08:54:57.492][biodb::testThat]
biodb.INFO [2024-06-10 08:54:57.494][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-10 08:54:57.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:57.496][biodb::testThat]
biodb.TRACE[2024-06-10 08:54:57.530][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.543][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:54:57.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:54:57.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:54:57.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:54:57.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.613][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.617][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:54:57.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:54:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:54:57.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:57.628][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:54:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:54:57.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:57.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:54:57.643][biodb::testThat]
biodb.INFO [2024-06-10 08:54:57.644][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-10 08:54:57.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:57.659][biodb::testThat]
biodb.INFO [2024-06-10 08:54:57.670][biodb::testThat]
biodb.INFO [2024-06-10 08:54:57.671][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-10 08:54:57.672][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:57.673][biodb::testThat]
biodb.INFO [2024-06-10 08:54:57.681][biodb::testThat]
biodb.INFO [2024-06-10 08:54:57.682][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-10 08:54:57.683][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:57.684][biodb::testThat]
biodb.DEBUG[2024-06-10 08:54:57.688][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-10 08:54:58.419][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-10 08:54:58.856][biodb::testThat]
biodb.INFO [2024-06-10 08:54:58.858][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-10 08:54:58.859][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:58.861][biodb::testThat]
biodb.TRACE[2024-06-10 08:54:58.874][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:58.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:58.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:58.881][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:58.883][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:58.885][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:58.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:58.887][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:54:58.890][biodb::testThat]
biodb.INFO [2024-06-10 08:54:58.891][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-10 08:54:58.894][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:58.896][biodb::testThat]
biodb.TRACE[2024-06-10 08:54:58.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:58.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:58.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:58.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:58.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:58.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:58.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:58.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:58.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:58.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:59.033][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-10 08:54:59.038][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:59.039][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-10 08:54:59.041][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:59.042][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-10 08:54:59.103][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-10 08:54:59.107][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:59.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-10 08:54:59.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:59.126][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-10 08:54:59.144][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:54:59.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:54:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:59.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:59.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:59.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:59.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:59.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:59.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:59.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:59.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:59.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:59.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:59.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:59.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:59.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:59.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:59.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:59.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:59.188][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-10 08:54:59.204][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:59.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:59.225][private$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[2024-06-10 08:55:03.159][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[2024-06-10 08:55:13.826][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:55:13.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-10 08:55:13.844][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-10 08:55:14.867][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[2024-06-10 08:55:14.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:14.873][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:14.875][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-10 08:55:15.470][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-10 08:55:16.061][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:55:16.064][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-10 08:55:16.071][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-10 08:55:16.103][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-10 08:55:16.107][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:16.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:16.110][private$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[2024-06-10 08:55:16.707][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[2024-06-10 08:55:17.574][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:55:17.577][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-10 08:55:17.583][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-10 08:55:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:17.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:17.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:17.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:55:17.622][biodb::testThat]
biodb.INFO [2024-06-10 08:55:17.623][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-10 08:55:17.625][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:55:17.625][biodb::testThat]
biodb.TRACE[2024-06-10 08:55:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:55:17.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:55:17.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:17.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:55:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:55:17.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:17.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:17.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:17.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:17.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:17.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:17.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:17.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:17.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:17.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:17.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:55:17.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:17.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:17.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:17.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:17.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:17.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:17.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:55:17.677][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[2024-06-10 08:55:17.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:17.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:17.685][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-10 08:55:21.711][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-10 08:55:31.721][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:55:31.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-10 08:55:31.759][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-10 08:55:32.742][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-10 08:55:32.785][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-10 08:55:32.787][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-10 08:55:32.789][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-10 08:55:32.790][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:55:32.791][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:55:32.792][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-10 08:55:32.793][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:55:32.794][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:55:32.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:32.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:32.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:32.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:32.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:32.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:32.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:55:32.823][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-10 08:55:32.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:32.827][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:32.829][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-10 08:55:33.372][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-06-10 08:55:33.983][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:55:33.988][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-06-10 08:55:33.997][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-06-10 08:55:34.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:34.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:34.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:34.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:34.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:34.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:34.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:55:34.025][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-10 08:55:34.030][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:34.031][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:34.033][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-10 08:55:34.637][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-10 08:55:35.226][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:55:35.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-10 08:55:35.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-10 08:55:35.238][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-10 08:55:35.240][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:55:35.241][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-10 08:55:35.242][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-10 08:55:35.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:35.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:35.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:35.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:35.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:35.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:35.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:35.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:55:35.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:55:35.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:55:35.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:55:35.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.280][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:55:35.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:55:35.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.285][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:55:35.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:55:35.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.290][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.296][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.300][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.312][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:55:35.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.318][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:55:35.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:55:35.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:55:35.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:55:35.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:55:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.345][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:55:35.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.351][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-10 08:55:35.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.366][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:55:35.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.376][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.384][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:55:35.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:35.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:35.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:35.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:35.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:35.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:35.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:35.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:55:35.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:55:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.449][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:55:35.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:55:35.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:55:35.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:55:35.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.462][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:55:35.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.537][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:55:35.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.542][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:55:35.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.545][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:55:35.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:55:35.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:55:35.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:55:35.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:55:35.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:55:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-10 08:55:35.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:55:35.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.588][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:55:35.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:55:35.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.592][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.607][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:55:35.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:55:35.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:55:35.659][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-10 08:55:35.674][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:55:35.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:35.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:35.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:35.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:35.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:35.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:35.688][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:55:35.689][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.693][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.697][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.698][private$selectFields]
biodb.TRACE[2024-06-10 08:55:35.699][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:35.700][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:35.701][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.703][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.705][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.706][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.708][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.709][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.711][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.712][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.713][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.714][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.715][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.719][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:35.720][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.726][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.731][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.749][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-10 08:55:35.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:35.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:35.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:35.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:35.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:35.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:35.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:35.768][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.777][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.778][private$selectFields]
biodb.TRACE[2024-06-10 08:55:35.779][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:35.779][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:35.780][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.781][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.782][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.788][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.789][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.791][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.792][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.792][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.793][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.794][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.795][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.796][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:35.797][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.800][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.805][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.809][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-10 08:55:35.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:35.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:35.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:35.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:35.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:35.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:35.830][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:55:35.833][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.839][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.842][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.843][private$selectFields]
biodb.TRACE[2024-06-10 08:55:35.844][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:35.844][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:35.847][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.848][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.850][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.852][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.853][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.854][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.857][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.859][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:35.860][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.861][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.862][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.863][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:35.864][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.869][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.872][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:35.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.877][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-10 08:55:35.878][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:55:35.879][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:55:35.893][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:35.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:35.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:55:35.942][biodb::testThat]
biodb.INFO [2024-06-10 08:55:35.944][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-10 08:55:35.946][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:55:35.947][biodb::testThat]
biodb.TRACE[2024-06-10 08:55:35.952][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:55:35.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:55:35.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:55:35.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:55:35.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:35.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:35.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:35.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:55:36.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:36.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:36.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:36.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:36.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:36.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:36.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:55:36.060][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[2024-06-10 08:55:36.068][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:36.069][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:36.072][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-06-10 08:55:40.112][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-06-10 08:55:50.252][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:55:50.256][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-10 08:55:50.275][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-10 08:55:51.811][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:55:51.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:51.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:51.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:51.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:51.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:51.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:51.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:51.854][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.858][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.880][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.881][private$selectFields]
biodb.TRACE[2024-06-10 08:55:51.882][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:51.883][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:51.884][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.885][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.886][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.888][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.889][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.890][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.892][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.893][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.904][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.905][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.906][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.909][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:51.910][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.914][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.917][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.922][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-10 08:55:51.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:51.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:51.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:51.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:51.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:51.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:51.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:51.936][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.945][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.946][private$selectFields]
biodb.TRACE[2024-06-10 08:55:51.947][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:51.948][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:51.949][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.951][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.952][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.955][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.955][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.957][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.958][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.959][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:51.960][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.961][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.964][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:51.965][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.969][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.973][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.978][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-10 08:55:51.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:51.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:51.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:51.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:51.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:51.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:51.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:51.991][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:51.996][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:51.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:51.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.000][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:52.001][private$selectFields]
biodb.TRACE[2024-06-10 08:55:52.002][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:52.004][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:52.005][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:52.007][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.008][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.011][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.012][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.014][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.015][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:52.016][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:52.017][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.018][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.020][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.021][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:52.022][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.031][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:52.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.035][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-10 08:55:52.036][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:55:52.037][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:55:52.048][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:52.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:52.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:55:52.057][biodb::testThat]
biodb.INFO [2024-06-10 08:55:52.059][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-10 08:55:52.060][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:55:52.061][biodb::testThat]
biodb.TRACE[2024-06-10 08:55:52.065][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:55:52.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:55:52.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:55:52.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:55:52.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:52.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:55:52.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:52.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:55:52.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:52.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:52.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:52.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:52.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:52.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:52.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:55:52.170][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-10 08:55:52.175][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:55:52.176][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-10 08:55:52.178][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:55:52.230][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-10 08:55:53.493][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:55:53.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:53.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:53.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:53.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:53.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:53.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:53.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:53.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.514][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.518][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.519][private$selectFields]
biodb.TRACE[2024-06-10 08:55:53.520][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:53.521][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:53.522][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.523][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.524][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.526][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.528][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.529][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.530][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.532][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.533][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.534][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.536][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.537][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:53.539][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.549][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-10 08:55:53.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:53.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:53.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:53.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:53.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:53.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:53.562][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:55:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.571][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.572][private$selectFields]
biodb.TRACE[2024-06-10 08:55:53.572][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:53.573][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:53.574][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.575][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.576][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.577][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.578][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.579][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.581][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.582][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.583][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.584][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.585][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.586][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.587][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:53.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.595][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.600][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.605][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-10 08:55:53.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:53.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:53.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:53.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:53.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:53.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:53.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:55:53.621][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.625][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.629][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.630][private$selectFields]
biodb.TRACE[2024-06-10 08:55:53.630][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:55:53.631][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:55:53.632][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.633][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.634][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.636][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.637][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.638][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.641][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.642][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.643][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:55:53.643][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.644][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.646][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.647][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-10 08:55:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.653][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:55:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:55:53.661][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-10 08:55:53.662][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:55:53.663][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:55:53.692][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:53.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:55:53.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:55:53.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:55:53.706][biodb::testThat]
biodb.INFO [2024-06-10 08:55:53.707][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-10 08:55:53.709][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:55:53.711][biodb::testThat]
biodb.DEBUG[2024-06-10 08:55:53.714][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-10 08:55:53.716][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:55:53.721][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-10 08:55:53.723][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:55:53.728][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:55:53.730][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:55:53.731][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-10 08:55:53.735][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:55:53.736][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:55:53.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:55:53.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:55:53.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:55:53.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:55:53.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:55:53.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:55:53.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:55:53.779][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-10 08:55:53.783][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:53.784][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:53.786][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:55:54.384][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:55:54.386][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:55:54.388][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:55:54.390][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:55:55.171][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:55:55.174][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:55.175][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:55.178][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:55:55.773][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:55:55.775][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:55:55.776][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:55:55.778][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:55:56.498][private$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[2024-06-10 08:55:56.500][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:56.501][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:56.503][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:55:57.083][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:55:57.085][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:55:57.086][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:55:57.087][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:55:58.006][private$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[2024-06-10 08:55:58.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:58.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:58.012][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:55:58.637][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:55:58.639][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:55:58.641][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:55:58.642][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:55:59.252][private$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[2024-06-10 08:55:59.253][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:55:59.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:55:59.257][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:55:59.889][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:55:59.892][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:55:59.894][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:55:59.896][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:56:00.706][private$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[2024-06-10 08:56:00.708][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:00.709][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:00.710][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:56:01.321][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:01.323][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:01.324][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:01.325][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:56:01.931][private$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[2024-06-10 08:56:01.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:01.935][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:01.937][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:56:02.521][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:02.523][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:02.524][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:02.525][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:56:03.064][private$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[2024-06-10 08:56:03.066][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:03.067][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:03.068][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:56:03.647][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:03.649][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:03.651][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:03.652][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:56:04.190][private$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[2024-06-10 08:56:04.192][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:04.194][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:04.197][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:56:04.769][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:04.771][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:04.772][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:04.774][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:56:05.548][private$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[2024-06-10 08:56:05.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:05.555][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:05.558][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-10 08:56:06.128][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:06.130][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:06.132][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:06.135][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-10 08:56:06.662][private$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[2024-06-10 08:56:06.666][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-10 08:56:06.669][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:56:06.671][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:56:06.672][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-10 08:56:06.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:56:06.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:06.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:06.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:06.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:06.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:06.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:56:06.690][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:06.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:06.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:06.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:06.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:06.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:06.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:06.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:06.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:06.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:06.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:06.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:06.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:06.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:06.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:06.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:06.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:06.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:06.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:06.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:06.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:06.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:56:06.724][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-10 08:56:06.724][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-10 08:56:06.738][biodb::testThat]
biodb.INFO [2024-06-10 08:56:06.740][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-10 08:56:06.741][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:06.742][biodb::testThat]
biodb.DEBUG[2024-06-10 08:56:06.755][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-10 08:56:06.757][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-10 08:56:06.758][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-10 08:56:06.761][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-10 08:56:06.762][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-10 08:56:06.764][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:56:06.765][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:56:06.767][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-10 08:56:06.768][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:56:06.771][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:56:06.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:56:06.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:06.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:06.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:06.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:06.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:06.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:06.790][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-10 08:56:06.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:06.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:06.796][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:07.335][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:07.336][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:07.338][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[2024-06-10 08:56:07.340][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:07.999][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:08.001][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:08.002][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:08.006][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:08.546][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:08.548][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:08.550][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[2024-06-10 08:56:08.551][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:09.083][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:09.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:09.086][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:09.088][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:09.635][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:09.636][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:09.639][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[2024-06-10 08:56:09.641][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:10.194][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:10.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:10.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:10.199][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:10.728][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:10.730][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:10.733][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[2024-06-10 08:56:10.734][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:11.343][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:11.345][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:11.346][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:11.347][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:11.913][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:11.915][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:11.916][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[2024-06-10 08:56:11.917][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:12.451][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:12.453][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:12.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:12.455][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:12.980][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:12.982][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:12.984][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[2024-06-10 08:56:12.985][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:13.572][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:13.574][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:13.575][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:13.576][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:14.168][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:14.169][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:14.173][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:14.175][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:14.732][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:14.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:14.734][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:14.737][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:15.331][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:15.333][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:15.338][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[2024-06-10 08:56:15.339][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:16.203][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:16.205][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:16.206][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:16.208][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:16.775][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:16.776][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:16.781][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[2024-06-10 08:56:16.782][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:17.563][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:17.565][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:17.566][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:17.568][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-10 08:56:18.107][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:18.110][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:18.111][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[2024-06-10 08:56:18.112][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-10 08:56:18.659][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:18.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:56:18.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:18.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:18.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:18.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:18.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:18.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:18.675][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-10 08:56:18.679][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:18.680][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:18.682][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:19.213][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:19.216][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:19.218][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:19.220][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:19.751][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:19.753][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:19.754][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:19.756][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:20.289][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:20.291][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:20.293][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:20.294][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:20.822][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:20.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:20.825][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:20.826][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:21.376][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:21.378][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:21.380][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:21.381][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:21.889][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:21.891][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:21.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:21.894][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:22.420][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:22.421][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:22.425][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:22.426][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:23.139][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:23.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:23.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:23.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:23.719][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:23.721][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:23.722][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:23.723][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:24.477][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:24.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:24.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:24.485][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:25.019][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:25.020][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:25.026][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:25.027][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:25.616][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:25.620][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:25.621][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:25.625][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:26.148][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:26.150][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:26.153][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:26.154][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:26.787][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:26.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:26.790][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:26.796][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:27.329][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:27.331][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:27.333][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:27.335][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:28.053][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:28.055][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:28.057][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:28.062][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:28.603][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:28.605][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:28.607][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:28.608][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:30.463][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-10 08:56:30.466][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:30.467][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:30.473][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-10 08:56:31.358][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-10 08:56:31.360][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-10 08:56:31.364][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-10 08:56:31.365][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-10 08:56:32.183][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-10 08:56:32.188][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-10 08:56:32.191][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:56:32.194][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-10 08:56:32.195][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-10 08:56:32.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:56:32.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:32.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:32.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:32.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:32.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:32.216][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:56:32.320][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.330][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:56:32.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:56:32.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:32.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:32.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:32.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:32.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:32.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:56:32.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.377][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:56:32.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:32.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:56:32.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:56:32.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:32.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:56:32.464][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-10 08:56:32.465][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-10 08:56:32.466][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-10 08:56:32.708][biodb::testThat]
biodb.INFO [2024-06-10 08:56:32.712][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-10 08:56:32.713][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:32.715][biodb::testThat]
biodb.INFO [2024-06-10 08:56:32.795][biodb::testThat]
biodb.INFO [2024-06-10 08:56:32.797][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-10 08:56:32.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:32.800][biodb::testThat]
biodb.INFO [2024-06-10 08:56:32.814][biodb::testThat]
biodb.INFO [2024-06-10 08:56:32.817][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-10 08:56:32.818][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:32.819][biodb::testThat]
biodb.DEBUG[2024-06-10 08:56:32.822][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[2024-06-10 08:56:32.827][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:32.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:32.830][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-10 08:56:36.892][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-10 08:56:46.997][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:56:47.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-10 08:56:47.016][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-10 08:56:47.952][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:56:47.954][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:56:47.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:47.961][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:56:47.962][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:56:47.967][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:56:47.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:56:47.969][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:56:47.975][biodb::testThat]
biodb.INFO [2024-06-10 08:56:47.976][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-10 08:56:47.978][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:47.980][biodb::testThat]
biodb.ERROR[2024-06-10 08:56:48.013][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-10 08:56:48.052][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-10 08:56:48.085][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 08:56:48.087][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-10 08:56:48.088][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-10 08:56:48.094][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 08:56:48.095][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:48.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:48.101][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.104][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 08:56:48.131][biodb::testContext]
biodb.INFO [2024-06-10 08:56:48.133][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:56:48.137][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-10 08:56:48.139][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:56:48.140][biodb::testContext]
biodb.INFO [2024-06-10 08:56:48.147][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:56:48.154][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 08:56:48.169][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:56:48.171][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 08:56:48.171][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 08:56:48.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.178][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 08:56:48.183][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 08:56:48.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.190][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 08:56:48.192][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 08:56:48.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.199][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[2024-06-10 08:56:48.200][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 08:56:48.204][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 08:56:48.206][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 08:56:48.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.214][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 08:56:48.219][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 08:56:48.220][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 08:56:48.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.228][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".
biodb.DEBUG[2024-06-10 08:56:48.228][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 08:56:48.232][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 08:56:48.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.239][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 08:56:48.241][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 08:56:48.242][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 08:56:48.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.255][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 08:56:48.256][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 08:56:48.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.262][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 08:56:48.263][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 08:56:48.268][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 08:56:48.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.276][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[2024-06-10 08:56:48.277][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:56:48.278][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 08:56:48.283][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 08:56:48.285][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 08:56:48.286][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 08:56:48.289][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 08:56:48.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.297][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 08:56:48.298][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 08:56:48.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.305][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[2024-06-10 08:56:48.307][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 08:56:48.308][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 08:56:48.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.317][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 08:56:48.319][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 08:56:48.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.327][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 08:56:48.328][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 08:56:48.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.335][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 08:56:48.336][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 08:56:48.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.341][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:56:48.346][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 08:56:48.389][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 08:56:48.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.398][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 08:56:48.400][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 08:56:48.401][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 08:56:48.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.404][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[2024-06-10 08:56:48.408][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 08:56:48.412][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.414][self$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[2024-06-10 08:56:48.415][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.420][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:56:48.421][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.422][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.427][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:56:48.431][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:56:48.432][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.434][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 08:56:48.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:56:48.438][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.439][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.443][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:56:48.443][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:56:48.443][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:56:48.443][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:56:48.443][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:56:48.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:56:48.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.450][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:56:48.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.456][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.457][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.458][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:56:48.461][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:56:48.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.464][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.467][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 08:56:48.469][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.473][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:56:48.475][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.476][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:56:48.480][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.482][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.483][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.486][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.487][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:56:48.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:56:48.493][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.494][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 08:56:48.497][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:56:48.498][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.500][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.504][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:56:48.504][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:56:48.504][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:56:48.504][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:56:48.504][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:56:48.506][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:56:48.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.511][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:56:48.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.519][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:56:48.524][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:56:48.525][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.529][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.531][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 08:56:48.534][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.536][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 08:56:48.537][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.540][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:56:48.542][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.543][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.543][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.546][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.548][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:56:48.549][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:56:48.549][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.553][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 08:56:48.554][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:56:48.555][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.556][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.560][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.562][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:56:48.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:56:48.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.645][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.646][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.647][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:56:48.648][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:56:48.650][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.651][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.653][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 08:56:48.658][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.659][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:56:48.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.662][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:56:48.663][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.663][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.664][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.669][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.671][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:56:48.672][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:56:48.674][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.676][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 08:56:48.677][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:56:48.677][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.682][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:48.683][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.684][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:56:48.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.689][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:56:48.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:48.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:48.695][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:56:48.696][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:56:48.702][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:56:48.703][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:48.704][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:48.707][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:56:48.709][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:48.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:48.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:48.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:48.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:48.861][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 08:56:48.865][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 08:56:48.867][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 08:56:48.873][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 08:56:48.874][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:56:48.876][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 08:56:48.878][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 08:56:48.880][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 08:56:48.885][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 08:56:48.888][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 08:56:48.894][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:56:48.896][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 08:56:48.898][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 08:56:48.899][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 08:56:48.901][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 08:56:48.905][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:56:48.907][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 08:56:48.910][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 08:56:48.912][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:56:48.916][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 08:56:48.917][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 08:56:48.919][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 08:56:48.922][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 08:56:48.924][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 08:56:48.925][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 08:56:48.927][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 08:56:48.929][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 08:56:48.934][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 08:56:48.935][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 08:56:48.937][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 08:56:48.941][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 08:56:48.943][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 08:56:48.947][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 08:56:48.948][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 08:56:48.949][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 08:56:48.953][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 08:56:48.954][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 08:56:48.958][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 08:56:48.960][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 08:56:48.962][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 08:56:48.965][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 08:56:48.967][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 08:56:48.972][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 08:56:48.973][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 08:56:48.977][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 08:56:48.979][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 08:56:48.980][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 08:56:48.984][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 08:56:48.986][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 08:56:48.989][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 08:56:48.991][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 08:56:48.992][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 08:56:48.996][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 08:56:48.997][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 08:56:48.998][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 08:56:49.002][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 08:56:49.004][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 08:56:49.008][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 08:56:49.010][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 08:56:49.013][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 08:56:49.015][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 08:56:49.019][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 08:56:49.021][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 08:56:49.023][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 08:56:49.029][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 08:56:49.031][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 08:56:49.033][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:56:49.035][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:56:49.039][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 08:56:49.041][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 08:56:49.045][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 08:56:49.047][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 08:56:49.050][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 08:56:49.052][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 08:56:49.055][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 08:56:49.057][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 08:56:49.059][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 08:56:49.063][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 08:56:49.064][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 08:56:49.070][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 08:56:49.071][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 08:56:49.073][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 08:56:49.079][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 08:56:49.090][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 08:56:49.092][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:56:49.096][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:56:49.097][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.099][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.204][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[2024-06-10 08:56:49.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.248][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[2024-06-10 08:56:49.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.265][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[2024-06-10 08:56:49.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:56:49.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:56:49.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:56:49.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:56:49.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:56:49.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:56:49.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:56:49.328][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[2024-06-10 08:56:49.332][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-10 08:56:49.337][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:56:49.340][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:49.343][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 08:56:49.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:49.345][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:56:49.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:49.351][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:56:49.352][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:49.355][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:56:49.356][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:56:49.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:56:49.362][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:49.363][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-10 08:56:49.364][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-10 08:56:49.366][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-10 08:56:49.368][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 08:56:49.369][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:56:49.369][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:56:49.370][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:56:49.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:49.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:49.376][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:56:49.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:56:49.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:56:49.381][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:56:49.382][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-10 08:56:49.382][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-10 08:56:49.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:56:49.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:56:49.388][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 08:56:49.389][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:56:49.392][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-10 08:56:49.394][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:56:49.401][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:56:49.404][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-10 08:56:49.406][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:56:49.408][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-10 08:56:49.410][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-10 08:56:49.411][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-10 08:56:49.416][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-10 08:56:49.417][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-10 08:56:49.421][biodb::testThat]
biodb.INFO [2024-06-10 08:56:49.422][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-10 08:56:49.423][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:49.423][biodb::testThat]
biodb.DEBUG[2024-06-10 08:56:49.432][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-06-10 08:56:49.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:49.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:49.446][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-10 08:56:50.044][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[2024-06-10 08:56:50.678][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:56:50.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-10 08:56:50.697][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-10 08:56:50.716][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[2024-06-10 08:56:50.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:50.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:50.730][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-10 08:56:51.616][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-10 08:56:52.234][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:56:52.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-10 08:56:52.243][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-10 08:56:52.258][biodb::testThat]
biodb.INFO [2024-06-10 08:56:52.259][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-10 08:56:52.260][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:52.261][biodb::testThat]
biodb.INFO [2024-06-10 08:56:52.292][biodb::testThat]
biodb.INFO [2024-06-10 08:56:52.293][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-10 08:56:52.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:56:52.295][biodb::testThat]
biodb.DEBUG[2024-06-10 08:56:52.298][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-10 08:56:52.302][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:52.303][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:52.305][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-10 08:56:52.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-10 08:56:53.204][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:56:53.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-10 08:56:53.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-10 08:56:53.234][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[2024-06-10 08:56:53.243][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:56:53.245][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-10 08:56:53.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:56:53.326][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-10 08:56:53.343][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[2024-06-10 08:56:53.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:53.352][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:53.357][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-10 08:56:53.857][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-10 08:56:54.326][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:56:54.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-10 08:56:54.346][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-10 08:56:54.363][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-06-10 08:56:54.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:54.374][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:54.376][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-10 08:56:55.597][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-10 08:56:58.672][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:56:58.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-10 08:56:58.690][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-10 08:56:58.890][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[2024-06-10 08:56:58.894][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:56:58.895][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:56:58.897][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-10 08:57:00.398][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-10 08:57:03.334][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:57:03.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-10 08:57:03.352][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-10 08:57:03.563][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 08:57:03.567][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-10 08:57:03.569][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-10 08:57:03.573][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 08:57:03.574][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:03.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:03.576][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:03.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:03.579][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 08:57:03.589][biodb::testContext]
biodb.INFO [2024-06-10 08:57:03.591][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:57:03.592][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-10 08:57:03.593][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:57:03.597][biodb::testContext]
biodb.INFO [2024-06-10 08:57:03.601][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:57:03.605][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 08:57:03.615][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:57:03.616][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 08:57:03.618][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 08:57:03.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.625][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.DEBUG[2024-06-10 08:57:03.626][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 08:57:03.628][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 08:57:03.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.636][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 08:57:03.637][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 08:57:03.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.647][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 08:57:03.649][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 08:57:03.650][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 08:57:03.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.661][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 08:57:03.662][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 08:57:03.668][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 08:57:03.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.674][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 08:57:03.675][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 08:57:03.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.686][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 08:57:03.687][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 08:57:03.689][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 08:57:03.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.699][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 08:57:03.701][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 08:57:03.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.711][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 08:57:03.712][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 08:57:03.713][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 08:57:03.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.717][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[2024-06-10 08:57:03.718][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:57:03.719][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 08:57:03.723][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 08:57:03.724][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 08:57:03.725][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 08:57:03.726][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 08:57:03.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.731][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 08:57:03.735][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 08:57:03.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.738][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[2024-06-10 08:57:03.739][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 08:57:03.742][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 08:57:03.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.748][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 08:57:03.750][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 08:57:03.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.756][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 08:57:03.757][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 08:57:03.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.763][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 08:57:03.767][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 08:57:03.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.773][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:57:03.774][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 08:57:03.820][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 08:57:03.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.829][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 08:57:03.830][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 08:57:03.832][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 08:57:03.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:03.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:03.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:03.840][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 08:57:03.843][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.846][self$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[2024-06-10 08:57:03.847][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.848][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:57:03.853][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.854][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.855][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.855][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.858][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:57:03.859][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:57:03.860][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.860][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 08:57:03.865][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:57:03.866][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:03.867][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.869][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:57:03.869][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:57:03.869][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:57:03.869][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:57:03.869][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:57:03.870][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:57:03.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:03.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:03.877][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:57:03.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:03.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:03.880][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.883][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:03.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:57:03.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:57:03.891][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.892][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:03.897][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 08:57:03.899][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.900][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:57:03.902][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.903][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:57:03.904][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.905][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.909][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.910][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.911][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:57:03.912][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:57:03.914][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.915][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 08:57:03.916][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:57:03.917][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:03.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.922][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:57:03.922][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:57:03.922][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:57:03.922][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:57:03.922][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:57:03.923][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:57:03.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:03.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:03.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:57:03.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:03.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:03.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.936][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:03.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:57:03.940][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:57:03.941][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.942][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:03.946][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 08:57:03.948][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.949][self$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[2024-06-10 08:57:03.953][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.954][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:57:03.955][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:03.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.959][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.960][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:57:03.961][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:57:03.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:57:03.966][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:03.967][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 08:57:04.051][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:57:04.052][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.056][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.058][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.059][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:57:04.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:04.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:04.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:57:04.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:04.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:04.072][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.073][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:57:04.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:57:04.077][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:04.082][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.084][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 08:57:04.088][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.089][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:57:04.091][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:57:04.095][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.097][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:04.101][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.102][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:57:04.103][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:57:04.107][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:04.108][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 08:57:04.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:57:04.113][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.114][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.115][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:57:04.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:04.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:04.122][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:57:04.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:04.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:04.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.131][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:57:04.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:57:04.136][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:04.138][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:57:04.143][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.176][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[2024-06-10 08:57:04.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.182][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[2024-06-10 08:57:04.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.193][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[2024-06-10 08:57:04.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.200][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[2024-06-10 08:57:04.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.214][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[2024-06-10 08:57:04.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.223][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[2024-06-10 08:57:04.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.238][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[2024-06-10 08:57:04.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.247][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[2024-06-10 08:57:04.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.256][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[2024-06-10 08:57:04.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.291][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 08:57:04.293][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 08:57:04.296][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 08:57:04.298][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 08:57:04.303][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:57:04.305][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 08:57:04.308][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 08:57:04.310][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 08:57:04.315][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 08:57:04.317][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 08:57:04.321][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:57:04.323][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 08:57:04.329][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 08:57:04.331][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 08:57:04.335][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 08:57:04.336][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:57:04.341][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 08:57:04.343][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 08:57:04.345][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:57:04.347][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 08:57:04.348][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 08:57:04.353][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 08:57:04.354][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 08:57:04.356][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 08:57:04.360][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 08:57:04.362][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 08:57:04.364][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 08:57:04.366][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 08:57:04.367][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 08:57:04.372][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 08:57:04.374][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 08:57:04.375][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 08:57:04.378][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 08:57:04.379][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 08:57:04.383][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 08:57:04.386][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 08:57:04.387][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 08:57:04.391][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 08:57:04.393][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 08:57:04.396][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 08:57:04.398][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 08:57:04.399][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 08:57:04.403][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 08:57:04.405][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 08:57:04.407][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 08:57:04.408][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 08:57:04.409][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 08:57:04.410][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 08:57:04.415][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 08:57:04.416][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 08:57:04.420][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 08:57:04.422][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 08:57:04.425][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 08:57:04.426][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 08:57:04.428][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 08:57:04.432][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 08:57:04.434][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 08:57:04.438][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 08:57:04.440][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 08:57:04.444][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 08:57:04.446][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 08:57:04.451][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 08:57:04.452][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 08:57:04.455][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 08:57:04.457][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 08:57:04.462][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 08:57:04.464][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:57:04.465][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:57:04.469][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 08:57:04.471][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 08:57:04.476][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 08:57:04.477][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 08:57:04.482][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 08:57:04.484][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 08:57:04.490][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 08:57:04.492][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 08:57:04.493][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 08:57:04.498][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 08:57:04.499][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 08:57:04.504][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 08:57:04.506][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 08:57:04.512][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 08:57:04.514][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 08:57:04.517][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 08:57:04.520][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:57:04.526][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:57:04.527][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.528][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.660][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[2024-06-10 08:57:04.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.698][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[2024-06-10 08:57:04.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.760][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[2024-06-10 08:57:04.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:57:04.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:04.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:04.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:04.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:04.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:04.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:57:04.777][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-10 08:57:04.781][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:57:04.784][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:04.788][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:57:04.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.796][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.797][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.800][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:57:04.802][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:57:04.803][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.807][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-10 08:57:04.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-10 08:57:04.809][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-10 08:57:04.812][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 08:57:04.814][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:57:04.814][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:57:04.815][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:57:04.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:04.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:04.820][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:57:04.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:57:04.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:57:04.826][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:57:04.827][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-10 08:57:04.827][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-10 08:57:04.830][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:57:04.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:57:04.833][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 08:57:04.834][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:57:04.837][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-10 08:57:04.838][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:57:04.845][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:57:04.846][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-10 08:57:04.850][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-10 08:57:04.851][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-10 08:57:04.855][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-10 08:57:04.857][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-10 08:57:04.858][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-10 08:57:04.862][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-10 08:57:04.863][biodb::testThat]
biodb.INFO [2024-06-10 08:57:04.864][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-10 08:57:04.868][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:57:04.869][biodb::testThat]
biodb.DEBUG[2024-06-10 08:57:04.876][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-10 08:57:04.883][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:57:04.887][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-10 08:57:04.888][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:57:04.943][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-10 08:57:06.394][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-10 08:57:06.399][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-10 08:57:06.427][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-10 08:57:06.430][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-10 08:57:06.434][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-10 08:57:06.436][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:57:06.441][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-10 08:57:06.443][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-10 08:57:06.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:57:06.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:06.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:06.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:06.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:06.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:06.465][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:57:06.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.509][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:57:06.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:57:06.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.516][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:57:06.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:57:06.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.534][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.555][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:57:06.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.562][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:57:06.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:06.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:06.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:06.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:06.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.605][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:57:06.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.616][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-10 08:57:06.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.639][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:57:06.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.683][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.691][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.707][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:57:06.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:57:06.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:06.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:06.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:06.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:06.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:06.759][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:57:06.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:06.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.801][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:57:06.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-10 08:57:06.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.807][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:57:06.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:57:06.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.815][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.824][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:06.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.837][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:06.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.841][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:57:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:06.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.845][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-10 08:57:06.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:06.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:06.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:06.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:06.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:06.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.910][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:57:06.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.915][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-10 08:57:06.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:06.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.929][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-10 08:57:06.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:06.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.939][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.951][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:06.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:06.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:06.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:06.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:06.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:57:07.005][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-06-10 08:57:07.008][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:57:07.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:57:07.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:07.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:07.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:07.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:07.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:07.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:57:07.023][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.028][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.032][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:57:07.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:57:07.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.036][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:57:07.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:57:07.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.040][private$selectFields] Fields none
biodb.TRACE[2024-06-10 08:57:07.041][private$selectFields]
biodb.TRACE[2024-06-10 08:57:07.042][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-10 08:57:07.043][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:57:07.044][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:57:07.045][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.047][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.048][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.049][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.052][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.053][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.055][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.056][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.057][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.059][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.059][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.060][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.062][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.063][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.064][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.066][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.067][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.069][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.070][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.071][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.073][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.074][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.076][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.077][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.078][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.080][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.081][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.082][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.083][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.084][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.085][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.086][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.087][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.088][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.090][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.091][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.092][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.093][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.094][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.097][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.098][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.100][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.101][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:57:07.101][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:57:07.102][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.105][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.108][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.109][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.110][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.112][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.113][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.115][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.116][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.119][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.120][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.121][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.122][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.123][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.125][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.127][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.128][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.130][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.131][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-10 08:57:07.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.166][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.172][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.185][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.190][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.250][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.265][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.268][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.272][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.281][private$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[2024-06-10 08:57:07.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:57:07.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:07.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:07.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:07.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:07.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:07.295][FUN] Functions in observer BiodbConfig: [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[2024-06-10 08:57:07.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:57:07.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:57:07.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:57:07.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.311][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:57:07.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:57:07.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.316][private$selectFields] Fields none
biodb.TRACE[2024-06-10 08:57:07.317][private$selectFields]
biodb.TRACE[2024-06-10 08:57:07.318][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-10 08:57:07.319][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:57:07.321][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:57:07.322][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.324][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.326][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.328][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.331][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.332][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.333][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.334][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.335][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.337][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.338][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.338][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.340][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.341][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.342][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.344][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.345][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.348][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.349][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.350][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.352][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.353][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.353][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.355][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.357][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.358][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.359][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.360][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.362][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.363][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.364][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.367][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.368][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.369][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.370][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.371][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.372][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.373][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.374][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.375][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.377][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.377][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:57:07.378][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-10 08:57:07.379][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.380][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.381][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.382][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.383][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.384][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.385][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.386][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.387][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.388][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.389][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.390][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.391][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.392][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.393][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.394][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.395][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.396][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.397][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.400][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.401][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.402][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.403][private$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[2024-06-10 08:57:07.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:57:07.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:57:07.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:57:07.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.429][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-10 08:57:07.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-10 08:57:07.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:57:07.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.460][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.502][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:57:07.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:57:07.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:57:07.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:57:07.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.518][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.521][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.525][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-10 08:57:07.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:57:07.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:57:07.532][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-06-10 08:57:07.533][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:57:07.534][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-10 08:57:07.541][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 08:57:07.543][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-10 08:57:07.544][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-10 08:57:07.545][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 08:57:07.546][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:57:07.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:57:07.547][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:57:07.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:57:07.549][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:57:07.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_generic.R:16:1'): One wrong entry does not block the retrieval of good ones ──
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.3380.6996.169
LipidmapsStructureEntry0.4280.0260.708