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This page was generated on 2024-05-30 11:35:26 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4518
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: 2024-05-29 14:00:10 -0400 (Wed, 29 May 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  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbLipidmaps on lconway


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: 2024-05-29 19:21:02 -0400 (Wed, 29 May 2024)
EndedAt: 2024-05-29 19:25:42 -0400 (Wed, 29 May 2024)
EllapsedTime: 279.1 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: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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
* 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 167 ]
  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-x86_64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-05-29 19:22:07.551][biodb::testContext]
biodb.INFO [2024-05-29 19:22:07.556][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:07.558][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-29 19:22:07.568][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:07.570][biodb::testContext]
biodb.INFO [2024-05-29 19:22:07.585][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:07.588][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:07.601][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:07.609][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-29 19:22:07.613][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-29 19:22:07.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.622][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-29 19:22:07.691][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-29 19:22:07.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.706][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-29 19:22:07.709][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-29 19:22:07.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.715][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-29 19:22:07.726][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-29 19:22:07.728][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-29 19:22:07.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.768][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[2024-05-29 19:22:07.770][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-29 19:22:07.779][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-29 19:22:07.780][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-29 19:22:07.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.787][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-29 19:22:07.799][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-29 19:22:07.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.804][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[2024-05-29 19:22:07.805][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-29 19:22:07.806][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-29 19:22:07.818][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-29 19:22:07.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.824][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-29 19:22:07.826][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-29 19:22:07.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.838][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[2024-05-29 19:22:07.840][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-29 19:22:07.841][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-29 19:22:07.843][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-29 19:22:07.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.858][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:07.859][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-29 19:22:07.861][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-29 19:22:07.862][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-29 19:22:07.864][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-29 19:22:07.875][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-29 19:22:07.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.881][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-29 19:22:07.894][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-29 19:22:07.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.902][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-29 19:22:07.903][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-29 19:22:07.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.918][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-29 19:22:07.920][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-29 19:22:07.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.938][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-29 19:22:07.939][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-29 19:22:07.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.955][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-29 19:22:07.957][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-29 19:22:07.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:07.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.969][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:07.971][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-29 19:22:08.004][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-29 19:22:08.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.010][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-29 19:22:08.011][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-29 19:22:08.013][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-29 19:22:08.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.022][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-29 19:22:08.108][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.147][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-29 19:22:08.149][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.150][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:08.158][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.160][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.161][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.162][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.164][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:08.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:08.175][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.177][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-29 19:22:08.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:08.180][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.183][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:08.183][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:08.183][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:08.183][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:08.183][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:08.185][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:08.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.196][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:08.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.200][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.201][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.210][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:08.212][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:08.214][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.216][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.217][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-29 19:22:08.228][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.230][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:08.232][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.233][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:08.235][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.236][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.245][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.247][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.249][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:08.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:08.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.253][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-29 19:22:08.255][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:08.269][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.271][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.273][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:08.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:08.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:08.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:08.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:08.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:08.276][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.287][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:08.288][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.291][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.292][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:08.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:08.306][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.307][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.309][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-29 19:22:08.312][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.313][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-29 19:22:08.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.325][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:08.326][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.328][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.329][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.330][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.332][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:08.344][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:08.346][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.362][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-29 19:22:08.364][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:08.365][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.367][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.368][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.378][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:08.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:08.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.397][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:08.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:08.402][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.403][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.406][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-29 19:22:08.417][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.419][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:08.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.422][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:08.423][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.424][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.432][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.435][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:08.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:08.438][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.440][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-29 19:22:08.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:08.450][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:08.454][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.455][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:08.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:08.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:08.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:08.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:08.475][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.485][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:08.487][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:08.492][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:08.493][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:08.507][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:08.508][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.609][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[2024-05-29 19:22:08.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.682][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[2024-05-29 19:22:08.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.703][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[2024-05-29 19:22:08.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:08.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:08.717][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-29 19:22:08.732][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-29 19:22:08.734][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-29 19:22:08.736][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-29 19:22:08.739][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:22:08.749][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-29 19:22:08.752][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:08.756][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:08.764][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-29 19:22:08.766][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-29 19:22:08.768][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:22:08.771][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-29 19:22:08.781][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:08.784][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:08.786][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-29 19:22:08.790][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:22:08.792][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-29 19:22:08.800][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-29 19:22:08.803][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:22:08.805][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-29 19:22:08.807][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-29 19:22:08.818][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-29 19:22:08.821][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-29 19:22:08.823][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-29 19:22:08.825][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-29 19:22:08.833][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-29 19:22:08.836][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-29 19:22:08.838][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-29 19:22:08.840][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-29 19:22:08.842][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-29 19:22:08.851][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-29 19:22:08.854][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-29 19:22:08.856][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-29 19:22:08.858][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-29 19:22:08.871][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-29 19:22:08.873][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-29 19:22:08.876][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-29 19:22:08.878][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-29 19:22:08.887][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-29 19:22:08.890][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-29 19:22:08.892][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-29 19:22:08.895][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-29 19:22:08.905][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-29 19:22:08.907][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-29 19:22:08.909][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-29 19:22:08.911][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-29 19:22:08.932][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-29 19:22:08.943][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-29 19:22:08.946][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-29 19:22:08.949][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-29 19:22:08.951][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-29 19:22:08.960][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-29 19:22:08.963][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-29 19:22:08.965][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-29 19:22:08.967][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-29 19:22:08.974][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-29 19:22:08.976][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-29 19:22:08.979][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-29 19:22:08.981][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-29 19:22:08.983][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-29 19:22:08.994][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-29 19:22:08.998][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-29 19:22:09.000][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-29 19:22:09.002][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-29 19:22:09.012][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-29 19:22:09.015][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-29 19:22:09.018][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:22:09.020][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:22:09.032][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-29 19:22:09.034][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-29 19:22:09.037][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-29 19:22:09.040][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-29 19:22:09.051][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-29 19:22:09.053][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-29 19:22:09.056][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-29 19:22:09.058][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-29 19:22:09.067][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-29 19:22:09.070][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-29 19:22:09.072][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-29 19:22:09.075][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-29 19:22:09.083][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-29 19:22:09.086][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-29 19:22:09.089][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-29 19:22:09.106][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-29 19:22:09.116][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:09.121][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:09.123][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.134][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.236][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[2024-05-29 19:22:09.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:09.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:09.504][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:09.544][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:22:09.548][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:09.556][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-29 19:22:09.558][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:09.559][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:09.561][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:09.563][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:09.572][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:09.574][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:09.576][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:09.577][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:09.579][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:09.581][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-29 19:22:09.591][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-29 19:22:09.593][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-29 19:22:09.595][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:09.597][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:09.597][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:09.599][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:09.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:09.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:09.612][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:09.614][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:09.615][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:09.623][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:09.625][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-29 19:22:09.625][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-29 19:22:09.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:09.628][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:09.630][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:09.632][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:09.659][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-29 19:22:09.662][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:22:09.748][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:22:09.750][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-29 19:22:09.766][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:22:09.779][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-29 19:22:09.794][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-29 19:22:09.796][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-29 19:22:09.799][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-29 19:22:09.801][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-29 19:22:09.831][biodb::testThat]
biodb.INFO [2024-05-29 19:22:09.833][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-29 19:22:09.843][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:09.846][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:09.854][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-05-29 19:22:09.858][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:09.871][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-29 19:22:09.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.958][FUN] Functions in observer BiodbConfig: [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[2024-05-29 19:22:09.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:09.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:10.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:10.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.083][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:22:10.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:22:10.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.099][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:10.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:10.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.116][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:10.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:10.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.214][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:10.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:10.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:10.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:10.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:10.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:22:10.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.295][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:22:10.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:10.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:10.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.317][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:10.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:10.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.334][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.358][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:22:10.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.370][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-29 19:22:10.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.405][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:22:10.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:10.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:10.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.626][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.633][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.662][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:10.809][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-29 19:22:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:22:10.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:22:10.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:22:10.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:22:10.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-29 19:22:10.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-29 19:22:10.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.852][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-29 19:22:10.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-29 19:22:10.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.950][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:10.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:10.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:10.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.053][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:11.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:11.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.068][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:11.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:11.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.077][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:11.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:11.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.146][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.148][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.165][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:11.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:11.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.218][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:11.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:11.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:11.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:11.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.241][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:11.249][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:11.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.253][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:11.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:11.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.309][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.328][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.343][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.350][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.360][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.363][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.365][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.394][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:11.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:11.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:11.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:11.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:11.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:11.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.435][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:11.436][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:11.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.439][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.449][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:11.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:11.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.521][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.523][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.527][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.573][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.580][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.592][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.605][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.607][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.612][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.642][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.651][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.654][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.669][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.670][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:11.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.673][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.698][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:11.699][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:11.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.702][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.715][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.717][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:11.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.742][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:11.744][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:11.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.747][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.757][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.759][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:11.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.761][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:11.812][biodb::testThat]
biodb.INFO [2024-05-29 19:22:11.814][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-29 19:22:11.815][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:11.817][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:11.850][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-29 19:22:11.868][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:11.876][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-05-29 19:22:11.878][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:11.880][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-05-29 19:22:11.881][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:11.945][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:11.947][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-29 19:22:11.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:11.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:11.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:11.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:11.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:11.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:11.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:11.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:11.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:11.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:11.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:11.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.031][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:22:12.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:22:12.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.043][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:12.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:12.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.055][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:12.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:12.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.062][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:12.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:22:12.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.075][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:12.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:12.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:12.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:22:12.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.097][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:22:12.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.110][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:22:12.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.123][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:12.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:12.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.130][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:12.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:12.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.163][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:22:12.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.178][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-29 19:22:12.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.227][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:22:12.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.296][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:12.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:12.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.308][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:12.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:12.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.329][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:12.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:22:12.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:12.420][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-29 19:22:12.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-29 19:22:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-29 19:22:12.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-29 19:22:12.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-29 19:22:12.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-29 19:22:12.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-29 19:22:12.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:12.482][biodb::testThat]
biodb.INFO [2024-05-29 19:22:12.484][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-29 19:22:12.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:12.487][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:12.505][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.508][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.511][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:12.520][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-29 19:22:12.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:12.645][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-29 19:22:12.659][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[2024-05-29 19:22:12.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:12.738][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:12.740][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-05-29 19:22:14.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-05-29 19:22:15.032][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:15.037][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-05-29 19:22:15.092][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-05-29 19:22:15.096][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-29 19:22:15.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.127][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:15.136][biodb::testThat]
biodb.INFO [2024-05-29 19:22:15.138][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-29 19:22:15.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:15.142][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:15.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:15.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:15.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:15.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:15.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:15.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:15.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.561][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-29 19:22:15.576][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:15.627][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-29 19:22:15.630][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:15.641][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-29 19:22:15.699][biodb::testThat]
biodb.INFO [2024-05-29 19:22:15.702][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-29 19:22:15.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:15.715][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:15.827][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:22:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:22:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.844][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:22:15.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:22:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-29 19:22:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-29 19:22:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.860][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-29 19:22:15.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-29 19:22:15.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:22:16.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:22:16.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.031][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:22:16.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:22:16.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.045][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-29 19:22:16.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-29 19:22:16.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-29 19:22:16.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-29 19:22:16.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:16.086][biodb::testThat]
biodb.INFO [2024-05-29 19:22:16.088][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-29 19:22:16.090][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:16.091][biodb::testThat]
biodb.INFO [2024-05-29 19:22:16.114][biodb::testThat]
biodb.INFO [2024-05-29 19:22:16.116][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-29 19:22:16.118][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:16.119][biodb::testThat]
biodb.INFO [2024-05-29 19:22:16.156][biodb::testThat]
biodb.INFO [2024-05-29 19:22:16.158][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-29 19:22:16.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:16.175][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:16.190][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-29 19:22:17.149][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-29 19:22:17.527][biodb::testThat]
biodb.INFO [2024-05-29 19:22:17.529][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-29 19:22:17.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:17.531][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:17.542][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:17.543][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:17.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.546][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.548][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.549][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.552][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:17.554][biodb::testThat]
biodb.INFO [2024-05-29 19:22:17.556][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-29 19:22:17.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:17.558][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:17.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:17.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:17.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:17.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:17.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:17.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:17.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.726][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-29 19:22:17.731][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:17.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-29 19:22:17.736][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:17.738][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-29 19:22:17.904][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-29 19:22:17.915][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:17.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-29 19:22:17.920][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:17.923][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-29 19:22:17.964][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:22:17.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:22:17.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:18.138][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-29 19:22:18.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:18.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:18.243][private$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[2024-05-29 19:22:22.194][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[2024-05-29 19:22:36.298][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-05-29 19:22:36.311][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-05-29 19:22:36.325][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-05-29 19:22:36.561][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-05-29 19:22:41.611][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-29 19:22:41.636][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:41.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:41.649][private$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[2024-05-29 19:22:42.237][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[2024-05-29 19:22:42.820][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:42.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-05-29 19:22:42.831][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-05-29 19:22:42.866][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[2024-05-29 19:22:42.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:42.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:42.879][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-05-29 19:22:43.470][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-05-29 19:22:44.134][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:44.138][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-05-29 19:22:44.162][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-05-29 19:22:44.265][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:44.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:44.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:44.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:44.294][biodb::testThat]
biodb.INFO [2024-05-29 19:22:44.296][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-29 19:22:44.297][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:44.298][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:22:44.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:22:44.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:44.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:44.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:44.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:44.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:44.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:44.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:44.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:44.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:44.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:44.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:44.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:44.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:44.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:44.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:44.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:44.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:44.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:44.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:44.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:44.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:44.437][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-29 19:22:44.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:44.479][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:44.491][private$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[2024-05-29 19:22:48.459][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[2024-05-29 19:22:58.556][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:58.560][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-05-29 19:22:58.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-05-29 19:23:02.684][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-29 19:23:02.746][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-29 19:23:02.748][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-29 19:23:02.750][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-29 19:23:02.751][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:23:02.753][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:23:02.755][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-29 19:23:02.756][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:23:02.757][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:23:02.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:02.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:02.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:02.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:02.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:02.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:02.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:23:02.790][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-05-29 19:23:02.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:02.796][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:02.797][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-29 19:23:03.386][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-05-29 19:23:03.986][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:23:04.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-05-29 19:23:04.036][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-05-29 19:23:04.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:04.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:04.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:04.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:04.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:04.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:04.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:23:04.060][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-05-29 19:23:04.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:04.065][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:04.067][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-05-29 19:23:04.672][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-05-29 19:23:05.259][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:23:05.261][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-05-29 19:23:05.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-05-29 19:23:05.269][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-05-29 19:23:05.272][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:23:05.273][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-29 19:23:05.275][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-29 19:23:05.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:05.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:05.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:05.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:05.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:05.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:05.318][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.TRACE[2024-05-29 19:23:05.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:23:05.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:23:05.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:23:05.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:23:05.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.349][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:23:05.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:23:05.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.354][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:23:05.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:23:05.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.369][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.377][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.383][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.391][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:23:05.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.398][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:23:05.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:05.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:23:05.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:23:05.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:23:05.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:23:05.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.439][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:23:05.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.450][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-29 19:23:05.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.475][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:23:05.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.484][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.492][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.517][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:23:05.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:05.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:05.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:05.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:05.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:05.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:05.608][FUN] Functions in observer BiodbConfig: [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[2024-05-29 19:23:05.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:23:05.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:23:05.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.687][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:23:05.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:23:05.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.697][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:23:05.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:23:05.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.774][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:23:05.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.780][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:23:05.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.801][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:23:05.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:05.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.813][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:23:05.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:05.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.825][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:23:05.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:23:05.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:23:05.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:23:05.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.861][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:23:05.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.867][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-29 19:23:05.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:23:05.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.890][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:23:05.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:23:05.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.910][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.917][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.928][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:05.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:05.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:05.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:05.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:23:05.988][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-29 19:23:06.001][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:23:06.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:06.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:06.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:06.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:06.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:06.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:06.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:23:06.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.045][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.049][private$selectFields]
biodb.TRACE[2024-05-29 19:23:06.051][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:06.054][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:06.068][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.070][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.074][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.077][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.080][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.081][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.095][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.097][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.099][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.100][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.101][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.104][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.119][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:06.123][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.138][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.145][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.181][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-29 19:23:06.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:06.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:06.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:06.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:06.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:06.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:06.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:23:06.211][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.216][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.237][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.239][private$selectFields]
biodb.TRACE[2024-05-29 19:23:06.240][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:06.242][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:06.248][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.250][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.252][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.254][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.256][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.257][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.260][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.261][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.263][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.264][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.266][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.268][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.268][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:06.269][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.273][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.285][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-29 19:23:06.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:06.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:06.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:06.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:06.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:06.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:06.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:23:06.305][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.311][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.318][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.320][private$selectFields]
biodb.TRACE[2024-05-29 19:23:06.321][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:06.322][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:06.324][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.325][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.327][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.331][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.348][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.351][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.355][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.357][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.358][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:06.360][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.361][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.391][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.392][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:06.394][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.403][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:06.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.433][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-29 19:23:06.435][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:23:06.437][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:23:06.473][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:23:06.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:23:06.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:23:06.537][biodb::testThat]
biodb.INFO [2024-05-29 19:23:06.539][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-29 19:23:06.551][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:23:06.553][biodb::testThat]
biodb.TRACE[2024-05-29 19:23:06.557][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:23:06.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:23:06.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:23:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:23:06.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:06.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:06.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:06.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:23:06.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:06.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:06.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:06.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:06.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:06.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:06.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:23:06.675][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-05-29 19:23:06.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:06.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:06.680][private$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[2024-05-29 19:23:10.613][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[2024-05-29 19:23:29.212][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:23:29.249][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-05-29 19:23:29.358][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-05-29 19:23:36.600][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:23:36.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:36.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:36.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:36.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:36.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:36.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:36.659][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.TRACE[2024-05-29 19:23:36.670][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.674][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.697][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.698][private$selectFields]
biodb.TRACE[2024-05-29 19:23:36.698][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:36.699][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:36.700][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.701][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.702][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.705][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.706][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.707][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.708][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.709][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.719][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.720][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.721][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.723][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.723][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:36.725][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.786][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.790][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-29 19:23:36.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:36.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:36.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:36.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:36.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:36.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:36.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:23:36.839][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.846][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.847][private$selectFields]
biodb.TRACE[2024-05-29 19:23:36.849][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:36.850][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:36.850][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.851][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.853][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.854][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.855][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.856][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.858][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.859][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.861][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:36.862][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.863][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.864][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.865][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:36.866][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.870][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.918][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.923][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-29 19:23:36.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:36.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:36.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:36.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:36.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:36.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:36.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:23:36.975][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.979][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:36.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:36.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:36.983][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:37.007][private$selectFields]
biodb.TRACE[2024-05-29 19:23:37.019][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:37.020][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:37.021][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:37.022][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.023][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.025][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.026][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.028][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.041][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.042][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:37.043][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:37.044][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.045][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.048][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:37.049][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.074][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.078][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:37.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.082][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-29 19:23:37.082][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:23:37.095][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:23:37.131][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:23:37.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:23:37.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:23:37.152][biodb::testThat]
biodb.INFO [2024-05-29 19:23:37.153][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-29 19:23:37.164][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:23:37.189][biodb::testThat]
biodb.TRACE[2024-05-29 19:23:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:23:37.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:23:37.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:23:37.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:23:37.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:37.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:23:37.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:37.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:23:37.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:37.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:37.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:37.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:37.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:37.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:37.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:23:37.422][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-29 19:23:37.425][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:23:37.426][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-29 19:23:37.427][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:23:37.503][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-29 19:23:40.615][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:23:40.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:40.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:40.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:40.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:40.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:40.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:40.628][FUN] Functions in observer BiodbConfig: [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[2024-05-29 19:23:40.629][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.661][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.662][private$selectFields]
biodb.TRACE[2024-05-29 19:23:40.663][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:40.664][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:40.665][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.666][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.667][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.668][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.669][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.670][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.672][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.673][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.674][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.674][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.675][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.677][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.678][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:40.679][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.683][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.686][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.690][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-29 19:23:40.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:40.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:40.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:40.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:40.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:40.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:40.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:23:40.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.716][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.720][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.721][private$selectFields]
biodb.TRACE[2024-05-29 19:23:40.722][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:40.723][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:40.724][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.725][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.737][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.740][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.741][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.742][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.745][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.745][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.746][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.747][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.749][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.750][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:40.751][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.755][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.759][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.764][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-29 19:23:40.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:40.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:40.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:40.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:40.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:40.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:40.775][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.TRACE[2024-05-29 19:23:40.776][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.780][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.783][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.784][private$selectFields]
biodb.TRACE[2024-05-29 19:23:40.785][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:23:40.786][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:23:40.787][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.788][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.789][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.790][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.791][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.792][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.794][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.794][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.795][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:23:40.812][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.813][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.815][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.816][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-29 19:23:40.817][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.828][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:40.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:40.831][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-29 19:23:40.832][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:23:40.833][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:23:40.883][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:23:40.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:23:40.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:40.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:23:40.893][biodb::testThat]
biodb.INFO [2024-05-29 19:23:40.893][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-29 19:23:40.894][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:23:40.895][biodb::testThat]
biodb.DEBUG[2024-05-29 19:23:40.897][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-29 19:23:40.897][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:23:40.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-29 19:23:40.900][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:23:40.901][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:23:40.902][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:23:40.903][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-29 19:23:40.904][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:23:40.904][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:23:40.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:40.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:40.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:40.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:40.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:40.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:40.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:23:40.931][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-05-29 19:23:40.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:40.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:40.958][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:41.515][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:41.521][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:41.523][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[2024-05-29 19:23:41.528][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:42.448][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:42.450][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:42.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:42.453][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:43.010][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:43.011][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:43.012][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[2024-05-29 19:23:43.013][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:43.573][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:43.574][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:43.576][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:43.578][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:44.135][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:44.136][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:44.137][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[2024-05-29 19:23:44.138][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:44.708][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:44.709][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:44.710][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:44.712][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:45.285][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:45.286][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:45.287][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[2024-05-29 19:23:45.299][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:45.898][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:45.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:45.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:45.904][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:46.470][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:46.489][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:46.490][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[2024-05-29 19:23:46.491][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:47.050][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:47.051][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:47.053][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:47.054][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:47.607][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:47.608][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:47.610][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[2024-05-29 19:23:47.612][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:48.189][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:48.190][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:48.191][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:48.193][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:48.759][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:48.760][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:48.763][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[2024-05-29 19:23:48.764][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:49.334][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:49.336][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:49.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:49.338][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:49.901][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:49.902][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:49.903][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[2024-05-29 19:23:49.905][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:50.424][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:50.425][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:50.426][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:50.427][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:50.945][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:50.947][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:50.948][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[2024-05-29 19:23:50.995][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:51.526][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:23:51.535][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:51.536][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:51.538][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-29 19:23:52.070][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:52.071][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:52.085][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[2024-05-29 19:23:52.086][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-29 19:23:52.596][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-29 19:23:52.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-05-29 19:23:52.604][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:23:52.606][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:23:52.607][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-29 19:23:52.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:52.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:52.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:52.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:52.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:52.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:52.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:23:52.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:52.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:52.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:52.633][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:52.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:23:52.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:52.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:52.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:52.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:52.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:52.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:52.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:52.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:52.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:52.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:52.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:52.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:52.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:52.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:23:52.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:23:52.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:23:52.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:23:52.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:23:52.662][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-29 19:23:52.663][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-29 19:23:52.679][biodb::testThat]
biodb.INFO [2024-05-29 19:23:52.681][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-29 19:23:52.682][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:23:52.683][biodb::testThat]
biodb.DEBUG[2024-05-29 19:23:52.709][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-29 19:23:52.710][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-29 19:23:52.711][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-29 19:23:52.715][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-29 19:23:52.717][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-29 19:23:52.720][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:23:52.721][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:23:52.722][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-29 19:23:52.723][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:23:52.724][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:23:52.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:23:52.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:23:52.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:23:52.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:23:52.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:23:52.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:23:52.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:23:52.743][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-05-29 19:23:52.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:52.746][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:52.748][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:23:53.266][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:53.268][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:53.269][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:23:53.270][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:23:54.051][private$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[2024-05-29 19:23:54.052][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:54.053][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:54.055][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:23:54.618][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:54.619][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:54.620][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:23:54.621][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:23:55.131][private$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[2024-05-29 19:23:55.132][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:55.133][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:55.134][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:23:55.707][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:55.708][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:55.709][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:23:55.710][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:23:56.228][private$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[2024-05-29 19:23:56.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:56.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:56.234][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:23:56.772][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:56.780][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:56.782][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:23:56.784][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:23:57.300][private$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[2024-05-29 19:23:57.302][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:57.304][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:57.306][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:23:57.824][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:57.825][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:57.827][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:23:57.829][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:23:58.466][private$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[2024-05-29 19:23:58.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:58.470][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:58.474][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:23:59.012][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:23:59.013][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:23:59.015][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:23:59.018][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:23:59.528][private$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[2024-05-29 19:23:59.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:23:59.530][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:23:59.532][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:24:00.151][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:00.152][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:00.174][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:24:00.175][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:24:00.708][private$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[2024-05-29 19:24:00.709][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:00.710][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:00.711][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:24:01.217][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:01.217][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:01.218][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:24:01.219][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:24:01.726][private$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[2024-05-29 19:24:01.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:01.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:01.728][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:24:02.234][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:02.235][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:02.236][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:24:02.247][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:24:02.757][private$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[2024-05-29 19:24:02.760][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:02.761][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:02.763][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-29 19:24:03.315][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:03.317][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:03.319][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:24:03.321][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-29 19:24:03.868][private$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[2024-05-29 19:24:03.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:24:03.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:24:03.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:24:03.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:24:03.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:24:03.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:03.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:03.930][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-05-29 19:24:03.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:03.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:03.950][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:04.466][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:04.467][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:04.468][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[2024-05-29 19:24:04.481][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:05.024][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:05.026][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:05.029][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:05.031][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:05.600][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:05.602][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:05.604][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[2024-05-29 19:24:05.607][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:06.606][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:06.607][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:06.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:06.610][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:07.126][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:07.127][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:07.128][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[2024-05-29 19:24:07.129][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:07.636][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:07.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:07.641][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:07.668][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:08.202][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:08.203][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:08.208][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[2024-05-29 19:24:08.222][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:08.789][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:08.791][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:08.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:08.793][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:09.311][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:09.312][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:09.313][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[2024-05-29 19:24:09.314][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:09.819][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:09.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:09.821][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:09.822][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:10.333][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:10.335][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:10.336][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[2024-05-29 19:24:10.337][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:11.082][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:11.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:11.086][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:11.087][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:11.604][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:11.607][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:11.609][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[2024-05-29 19:24:11.611][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:12.537][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:12.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:12.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:12.543][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:13.086][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:13.088][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:13.090][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[2024-05-29 19:24:13.091][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:13.661][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:13.664][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:13.666][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:13.668][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:14.195][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:14.197][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:14.200][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[2024-05-29 19:24:14.202][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:14.814][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:24:14.816][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:14.819][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:14.821][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-29 19:24:15.605][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:24:15.607][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:24:15.609][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[2024-05-29 19:24:15.611][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-29 19:24:16.162][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-29 19:24:16.168][private$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[2024-05-29 19:24:16.171][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:24:16.174][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-29 19:24:16.187][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-29 19:24:16.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:24:16.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:24:16.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:24:16.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:24:16.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:24:16.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:16.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:24:16.462][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.466][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:24:16.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:24:16.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:24:16.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:24:16.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:24:16.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:24:16.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:16.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:24:16.483][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.487][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:24:16.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:16.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:24:16.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:24:16.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:16.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:24:16.554][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-29 19:24:16.568][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-29 19:24:16.570][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-29 19:24:21.428][biodb::testThat]
biodb.INFO [2024-05-29 19:24:21.459][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-29 19:24:21.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:24:21.488][biodb::testThat]
biodb.INFO [2024-05-29 19:24:21.642][biodb::testThat]
biodb.INFO [2024-05-29 19:24:21.657][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-29 19:24:21.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:24:21.659][biodb::testThat]
biodb.INFO [2024-05-29 19:24:21.691][biodb::testThat]
biodb.INFO [2024-05-29 19:24:21.692][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-29 19:24:21.693][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:24:21.695][biodb::testThat]
biodb.DEBUG[2024-05-29 19:24:21.778][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-29 19:24:21.878][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:24:21.879][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:24:21.881][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-05-29 19:24:26.032][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-05-29 19:24:42.899][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:24:43.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-05-29 19:24:43.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-05-29 19:24:59.458][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:24:59.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:24:59.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:59.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:24:59.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:24:59.462][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:24:59.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:24:59.464][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:24:59.521][biodb::testThat]
biodb.INFO [2024-05-29 19:24:59.522][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-29 19:24:59.523][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:24:59.524][biodb::testThat]
biodb.ERROR[2024-05-29 19:24:59.550][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-29 19:24:59.592][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-29 19:24:59.604][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-29 19:24:59.605][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-29 19:24:59.606][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-29 19:24:59.607][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-29 19:24:59.608][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:24:59.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:24:59.609][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:24:59.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:24:59.610][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.611][FUN] Functions in observer BiodbConfig: [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 [2024-05-29 19:24:59.648][biodb::testContext]
biodb.INFO [2024-05-29 19:24:59.649][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:24:59.650][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-29 19:24:59.651][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:24:59.652][biodb::testContext]
biodb.INFO [2024-05-29 19:24:59.657][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:24:59.660][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-29 19:24:59.667][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:24:59.668][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-29 19:24:59.668][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-29 19:24:59.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.673][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-29 19:24:59.674][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-29 19:24:59.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.676][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-29 19:24:59.677][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-29 19:24:59.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.680][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-29 19:24:59.681][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-29 19:24:59.682][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-29 19:24:59.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.685][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-29 19:24:59.686][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-29 19:24:59.687][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-29 19:24:59.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.690][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-29 19:24:59.691][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-29 19:24:59.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.694][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-29 19:24:59.695][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-29 19:24:59.696][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-29 19:24:59.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.698][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-29 19:24:59.699][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-29 19:24:59.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.702][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-29 19:24:59.703][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-29 19:24:59.703][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-29 19:24:59.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.707][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:24:59.708][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-29 19:24:59.709][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-29 19:24:59.710][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-29 19:24:59.711][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-29 19:24:59.711][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-29 19:24:59.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.713][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[2024-05-29 19:24:59.714][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-29 19:24:59.715][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-29 19:24:59.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.718][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-29 19:24:59.745][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-29 19:24:59.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.748][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[2024-05-29 19:24:59.750][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-29 19:24:59.750][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-29 19:24:59.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.754][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-29 19:24:59.754][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-29 19:24:59.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.783][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[2024-05-29 19:24:59.785][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-29 19:24:59.786][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-29 19:24:59.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.791][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:24:59.792][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-29 19:24:59.857][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-29 19:24:59.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:24:59.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:24:59.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:24:59.958][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-29 19:25:00.027][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-29 19:25:00.028][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-29 19:25:00.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.099][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-29 19:25:00.101][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.103][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-29 19:25:00.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:00.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.146][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.226][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:25:00.228][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:00.229][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.274][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-29 19:25:00.276][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:00.300][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.314][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.337][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:25:00.337][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:25:00.337][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:25:00.337][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:25:00.337][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:25:00.340][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:00.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.342][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:00.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.346][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:00.348][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:00.348][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.360][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.390][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-29 19:25:00.392][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.393][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:25:00.394][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:00.395][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.396][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.397][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.398][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.399][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:25:00.400][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:00.401][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.402][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-29 19:25:00.403][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:00.404][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.405][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.406][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:25:00.406][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:25:00.406][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:25:00.406][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:25:00.406][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:25:00.407][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:00.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:00.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.448][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.449][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:00.450][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:00.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.451][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.453][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-29 19:25:00.468][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.514][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-29 19:25:00.528][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.529][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:00.530][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.531][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.532][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.534][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:25:00.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:00.536][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.537][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-29 19:25:00.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:00.540][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.547][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.548][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.549][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:00.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.606][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:00.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.608][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.609][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:00.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:00.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.617][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.619][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-29 19:25:00.621][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.621][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:25:00.622][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:00.624][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.625][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.626][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.627][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.628][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:25:00.630][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:00.631][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.632][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-29 19:25:00.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:00.635][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.636][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:00.637][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.638][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:00.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.642][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:00.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:00.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:00.644][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:00.645][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.646][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:00.646][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:00.647][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:00.648][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:00.651][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:25:00.652][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.660][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[2024-05-29 19:25:00.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.668][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[2024-05-29 19:25:00.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.672][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[2024-05-29 19:25:00.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.719][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[2024-05-29 19:25:00.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.756][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-29 19:25:00.760][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-29 19:25:00.761][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-29 19:25:00.763][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-29 19:25:00.765][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:25:00.766][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-29 19:25:00.767][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-29 19:25:00.768][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-29 19:25:00.772][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-29 19:25:00.774][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-29 19:25:00.776][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:25:00.777][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-29 19:25:00.779][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-29 19:25:00.780][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-29 19:25:00.785][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-29 19:25:00.789][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:25:00.791][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-29 19:25:00.793][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-29 19:25:00.795][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:25:00.797][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-29 19:25:00.798][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-29 19:25:00.800][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-29 19:25:00.802][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-29 19:25:00.804][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-29 19:25:00.806][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-29 19:25:00.808][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-29 19:25:00.810][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-29 19:25:00.811][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-29 19:25:00.813][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-29 19:25:00.814][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-29 19:25:00.815][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-29 19:25:00.817][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-29 19:25:00.818][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-29 19:25:00.819][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-29 19:25:00.821][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-29 19:25:00.822][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-29 19:25:00.823][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-29 19:25:00.824][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-29 19:25:00.826][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-29 19:25:00.829][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-29 19:25:00.833][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-29 19:25:00.834][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-29 19:25:00.836][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-29 19:25:00.837][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-29 19:25:00.838][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-29 19:25:00.840][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-29 19:25:00.841][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-29 19:25:00.842][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-29 19:25:00.844][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-29 19:25:00.846][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-29 19:25:00.848][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-29 19:25:00.850][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-29 19:25:00.853][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-29 19:25:00.854][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-29 19:25:00.855][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-29 19:25:00.857][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-29 19:25:00.859][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-29 19:25:00.861][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-29 19:25:00.862][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-29 19:25:00.863][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-29 19:25:00.865][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-29 19:25:00.879][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-29 19:25:00.881][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-29 19:25:00.882][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-29 19:25:00.883][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-29 19:25:00.885][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-29 19:25:00.886][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:25:00.887][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:25:00.888][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-29 19:25:00.892][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-29 19:25:00.894][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-29 19:25:00.896][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-29 19:25:00.897][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-29 19:25:00.900][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-29 19:25:00.901][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-29 19:25:00.903][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-29 19:25:00.905][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-29 19:25:00.907][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-29 19:25:00.909][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-29 19:25:00.911][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-29 19:25:00.913][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-29 19:25:00.914][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-29 19:25:00.916][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-29 19:25:00.918][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-29 19:25:00.921][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:25:00.923][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:25:00.928][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.932][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:00.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:00.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:00.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:00.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:00.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:00.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:00.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:00.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:00.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:00.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:00.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:00.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:00.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:00.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:00.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:01.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:01.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:01.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:01.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:01.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:01.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:01.082][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-29 19:25:01.085][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:25:01.088][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:01.089][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-29 19:25:01.090][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:01.091][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:01.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:01.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:01.093][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:01.094][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:01.095][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:25:01.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:01.097][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:01.098][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-29 19:25:01.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-29 19:25:01.100][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-29 19:25:01.101][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:01.102][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:25:01.102][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:25:01.103][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:01.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:01.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:01.107][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:01.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:01.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:01.110][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:01.111][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-29 19:25:01.111][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-29 19:25:01.112][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:01.113][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:01.114][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:01.115][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:01.119][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-29 19:25:01.121][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:25:01.126][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:25:01.126][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-29 19:25:01.129][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:25:01.131][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-29 19:25:01.136][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-29 19:25:01.137][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-29 19:25:01.138][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-29 19:25:01.139][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-29 19:25:01.140][biodb::testThat]
biodb.INFO [2024-05-29 19:25:01.141][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-29 19:25:01.142][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:25:01.143][biodb::testThat]
biodb.DEBUG[2024-05-29 19:25:01.152][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[2024-05-29 19:25:01.156][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:01.158][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:01.174][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-05-29 19:25:01.761][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-05-29 19:25:02.341][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:25:02.348][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-05-29 19:25:02.357][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-05-29 19:25:02.413][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-05-29 19:25:02.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:02.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:02.429][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-05-29 19:25:03.026][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[2024-05-29 19:25:03.899][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:25:03.902][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-05-29 19:25:03.913][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-05-29 19:25:03.955][biodb::testThat]
biodb.INFO [2024-05-29 19:25:03.957][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-29 19:25:03.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:25:03.971][biodb::testThat]
biodb.INFO [2024-05-29 19:25:04.073][biodb::testThat]
biodb.INFO [2024-05-29 19:25:04.076][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-29 19:25:04.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:25:04.084][biodb::testThat]
biodb.DEBUG[2024-05-29 19:25:04.089][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[2024-05-29 19:25:04.101][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:04.104][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:04.108][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-05-29 19:25:04.579][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-05-29 19:25:04.996][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:25:04.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-05-29 19:25:05.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-05-29 19:25:05.009][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-29 19:25:05.011][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:25:05.013][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-29 19:25:05.014][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:25:05.020][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-29 19:25:05.037][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-05-29 19:25:05.040][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:05.041][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-29 19:25:05.042][rule$waitAsNeeded] Wait 0.0637891 second(s).
biodb.TRACE[2024-05-29 19:25:05.238][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-05-29 19:25:05.750][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-05-29 19:25:06.221][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:25:06.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-05-29 19:25:06.257][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-05-29 19:25:06.264][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-05-29 19:25:06.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:06.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:06.269][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-05-29 19:25:07.450][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-05-29 19:25:10.615][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:25:10.617][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-05-29 19:25:10.636][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-05-29 19:25:10.957][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[2024-05-29 19:25:10.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:10.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:10.967][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-05-29 19:25:12.167][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-05-29 19:25:15.026][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:25:15.029][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-05-29 19:25:15.044][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-05-29 19:25:15.338][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-29 19:25:15.340][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-29 19:25:15.342][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-29 19:25:15.343][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-29 19:25:15.344][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:15.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:15.345][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.348][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-29 19:25:15.355][biodb::testContext]
biodb.INFO [2024-05-29 19:25:15.356][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:25:15.357][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-29 19:25:15.358][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:25:15.359][biodb::testContext]
biodb.INFO [2024-05-29 19:25:15.362][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:25:15.364][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-29 19:25:15.372][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:25:15.373][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-29 19:25:15.375][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-29 19:25:15.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.380][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-29 19:25:15.381][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-29 19:25:15.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.384][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-29 19:25:15.386][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-29 19:25:15.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.390][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-29 19:25:15.391][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-29 19:25:15.392][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-29 19:25:15.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.396][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-29 19:25:15.398][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-29 19:25:15.399][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-29 19:25:15.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.404][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-29 19:25:15.405][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-29 19:25:15.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.409][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-29 19:25:15.410][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-29 19:25:15.412][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-29 19:25:15.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.415][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-29 19:25:15.416][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-29 19:25:15.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.421][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-29 19:25:15.422][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-29 19:25:15.423][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-29 19:25:15.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.427][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:25:15.429][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-29 19:25:15.430][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-29 19:25:15.431][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-29 19:25:15.433][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-29 19:25:15.434][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-29 19:25:15.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.438][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-29 19:25:15.439][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-29 19:25:15.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.443][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-29 19:25:15.444][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-29 19:25:15.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.449][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-29 19:25:15.450][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-29 19:25:15.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.455][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-29 19:25:15.456][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-29 19:25:15.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.461][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-29 19:25:15.462][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-29 19:25:15.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.467][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:25:15.470][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-29 19:25:15.494][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-29 19:25:15.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.498][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-29 19:25:15.500][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-29 19:25:15.501][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-29 19:25:15.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.506][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-29 19:25:15.509][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.510][self$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[2024-05-29 19:25:15.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.514][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:15.515][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.517][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.519][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:25:15.520][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:15.522][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.523][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-29 19:25:15.525][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:15.526][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.528][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.530][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:25:15.530][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:25:15.530][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:25:15.530][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:25:15.530][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:25:15.531][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:15.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.535][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:15.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.538][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.539][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.540][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:15.541][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:15.542][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.543][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.544][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-29 19:25:15.546][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.547][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:25:15.548][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.549][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:15.550][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.550][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.552][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.553][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.554][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:25:15.554][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:15.555][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.556][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-29 19:25:15.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:15.559][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.560][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.561][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:25:15.561][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:25:15.561][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:25:15.561][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:25:15.561][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:25:15.562][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:15.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:15.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.570][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:15.572][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:15.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.574][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.576][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-29 19:25:15.577][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.578][self$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[2024-05-29 19:25:15.579][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.580][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:15.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.582][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.584][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.586][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:25:15.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:15.589][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.590][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-29 19:25:15.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:15.592][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.594][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.595][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:15.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:15.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.604][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.606][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.608][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:15.608][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:15.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.610][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.611][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-29 19:25:15.613][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.615][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:25:15.616][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.617][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:15.619][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.620][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.650][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.653][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:25:15.654][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:15.655][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.657][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-29 19:25:15.658][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:15.660][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.661][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:15.662][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.663][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:15.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.666][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.667][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:15.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:15.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:15.671][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:15.672][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.673][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:15.674][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:15.675][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:15.677][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:15.678][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:25:15.679][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.690][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[2024-05-29 19:25:15.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.694][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[2024-05-29 19:25:15.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.708][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[2024-05-29 19:25:15.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.735][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[2024-05-29 19:25:15.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.746][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[2024-05-29 19:25:15.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.767][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.DEBUG[2024-05-29 19:25:15.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.773][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-29 19:25:15.775][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-29 19:25:15.776][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-29 19:25:15.778][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-29 19:25:15.780][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:25:15.782][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-29 19:25:15.784][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-29 19:25:15.785][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-29 19:25:15.787][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-29 19:25:15.788][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-29 19:25:15.790][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:25:15.792][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-29 19:25:15.794][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-29 19:25:15.796][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-29 19:25:15.797][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-29 19:25:15.799][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:25:15.801][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-29 19:25:15.802][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-29 19:25:15.805][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:25:15.806][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-29 19:25:15.808][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-29 19:25:15.809][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-29 19:25:15.811][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-29 19:25:15.812][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-29 19:25:15.813][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-29 19:25:15.815][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-29 19:25:15.817][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-29 19:25:15.819][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-29 19:25:15.820][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-29 19:25:15.822][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-29 19:25:15.824][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-29 19:25:15.826][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-29 19:25:15.828][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-29 19:25:15.830][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-29 19:25:15.832][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-29 19:25:15.834][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-29 19:25:15.836][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-29 19:25:15.838][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-29 19:25:15.840][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-29 19:25:15.842][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-29 19:25:15.843][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-29 19:25:15.845][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-29 19:25:15.847][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-29 19:25:15.849][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-29 19:25:15.851][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-29 19:25:15.853][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-29 19:25:15.855][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-29 19:25:15.857][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-29 19:25:15.859][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-29 19:25:15.862][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-29 19:25:15.864][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-29 19:25:15.866][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-29 19:25:15.869][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-29 19:25:15.871][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-29 19:25:15.874][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-29 19:25:15.876][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-29 19:25:15.877][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-29 19:25:15.879][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-29 19:25:15.881][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-29 19:25:15.883][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-29 19:25:15.885][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-29 19:25:15.887][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-29 19:25:15.889][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-29 19:25:15.891][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-29 19:25:15.893][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-29 19:25:15.895][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-29 19:25:15.897][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:25:15.899][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:25:15.901][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-29 19:25:15.903][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-29 19:25:15.904][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-29 19:25:15.906][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-29 19:25:15.908][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-29 19:25:15.911][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-29 19:25:15.913][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-29 19:25:15.915][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-29 19:25:15.917][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-29 19:25:15.919][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-29 19:25:15.921][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-29 19:25:15.923][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-29 19:25:15.924][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-29 19:25:15.926][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-29 19:25:15.928][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-29 19:25:15.929][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-29 19:25:15.932][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:25:15.933][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:25:15.935][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.937][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:15.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:15.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:15.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:15.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:15.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:15.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:15.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:15.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:15.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:15.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:15.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:15.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:15.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:15.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:15.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:15.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:15.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:16.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:25:16.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:16.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:16.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:16.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:16.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:16.104][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.DEBUG[2024-05-29 19:25:16.109][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-29 19:25:16.111][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:25:16.113][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:16.115][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-29 19:25:16.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:16.117][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:25:16.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:16.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:25:16.120][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:16.120][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:25:16.121][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:25:16.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:25:16.123][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:16.124][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-29 19:25:16.126][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-29 19:25:16.127][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-29 19:25:16.129][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-29 19:25:16.130][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:25:16.130][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:25:16.131][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:25:16.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:16.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:16.134][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:25:16.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:25:16.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:25:16.137][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:25:16.138][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-29 19:25:16.138][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-29 19:25:16.138][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:25:16.139][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:25:16.140][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-29 19:25:16.141][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:25:16.142][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-29 19:25:16.143][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:25:16.147][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:25:16.149][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-29 19:25:16.150][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-29 19:25:16.153][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-29 19:25:16.155][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-29 19:25:16.156][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-29 19:25:16.158][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-29 19:25:16.159][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-29 19:25:16.161][biodb::testThat]
biodb.INFO [2024-05-29 19:25:16.162][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-29 19:25:16.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:25:16.164][biodb::testThat]
biodb.DEBUG[2024-05-29 19:25:16.167][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-29 19:25:16.171][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:25:16.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-29 19:25:16.173][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:25:16.278][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-29 19:25:18.238][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-29 19:25:18.240][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-29 19:25:18.242][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-29 19:25:18.243][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2024-05-29 19:25:18.245][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-05-29 19:25:18.247][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:25:18.249][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-29 19:25:18.250][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:25:18.251][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:25:18.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:25:18.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:18.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:18.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:18.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:18.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:18.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:25:18.265][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-05-29 19:25:18.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:18.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:18.269][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:18.839][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:18.840][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:18.842][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:18.844][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:19.614][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:19.616][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:19.617][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:19.621][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:20.141][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:20.143][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:20.144][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:20.146][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:20.670][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:20.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:20.673][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:20.674][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:21.194][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:21.196][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:21.198][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:21.199][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:21.714][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:21.716][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:21.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:21.719][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:22.230][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:22.232][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:22.233][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:22.234][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:22.740][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:22.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:22.743][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:22.745][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:23.250][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:23.251][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:23.252][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:23.254][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:23.868][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:23.892][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:23.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:23.895][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:24.426][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:24.428][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:24.429][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:24.431][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:25.003][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:25.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:25.006][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:25.008][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:25.528][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:25.530][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:25.531][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:25.533][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:26.046][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:26.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:26.048][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:26.049][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:26.557][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:26.558][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:26.569][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:26.570][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:27.084][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:27.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:27.087][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:27.088][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:27.593][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:27.594][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:27.595][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:27.596][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:28.104][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-29 19:25:28.106][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:25:28.107][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:25:28.109][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-29 19:25:28.606][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-29 19:25:28.607][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-29 19:25:28.609][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-29 19:25:28.611][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-29 19:25:29.124][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-29 19:25:29.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2024-05-29 19:25:29.130][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:25:29.132][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-29 19:25:29.134][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-29 19:25:29.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:25:29.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:29.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:29.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:29.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:29.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:29.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:25:29.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:25:29.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:25:29.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:29.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:29.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:29.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:29.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:29.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:25:29.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.210][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:25:29.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-29 19:25:29.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.215][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:25:29.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:25:29.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.221][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.232][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.243][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:25:29.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.248][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-29 19:25:29.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.276][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:25:29.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-29 19:25:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.295][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-29 19:25:29.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.301][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.361][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:25:29.424][self$createEntryFromContent] Accession numbers: NA, LMFA00000002.
biodb.DEBUG[2024-05-29 19:25:29.425][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-29 19:25:29.427][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:25:29.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:25:29.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:29.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:29.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:29.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:29.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:29.441][FUN] Functions in observer BiodbConfig: [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[2024-05-29 19:25:29.442][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-05-29 19:25:29.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:25:29.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:29.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:29.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:29.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:29.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:29.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:25:29.458][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:25:29.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:25:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.463][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:25:29.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:25:29.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.467][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-29 19:25:29.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-29 19:25:29.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.473][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-29 19:25:29.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-29 19:25:29.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.479][private$selectFields] Fields none
biodb.TRACE[2024-05-29 19:25:29.480][private$selectFields]
biodb.TRACE[2024-05-29 19:25:29.482][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-29 19:25:29.483][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:25:29.485][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:25:29.486][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.487][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.489][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.490][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.492][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.494][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.495][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.496][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.498][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.499][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.500][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.502][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.503][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.505][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.507][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.509][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.510][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.512][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.513][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.514][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.517][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.519][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.521][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.522][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.524][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.525][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.530][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.531][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.532][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.534][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.535][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.536][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.538][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.539][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.541][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.544][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.548][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.549][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.551][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.553][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.555][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.556][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.558][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.559][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:25:29.560][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-29 19:25:29.561][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.562][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.565][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.567][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.570][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.571][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.572][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.574][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.575][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.576][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.579][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.580][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.581][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.583][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.584][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.585][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.589][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.590][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.592][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.593][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.594][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.597][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.598][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-29 19:25:29.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:25:29.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:25:29.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:25:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.639][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-29 19:25:29.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.643][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.649][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-29 19:25:29.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:25:29.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.694][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:25:29.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:25:29.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:25:29.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:25:29.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.722][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.733][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-29 19:25:29.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:25:29.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:25:29.751][private$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[2024-05-29 19:25:29.753][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:25:29.754][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-29 19:25:29.763][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-29 19:25:29.765][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-29 19:25:29.767][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-29 19:25:29.768][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-29 19:25:29.769][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:25:29.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:25:29.770][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:25:29.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:25:29.773][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:25:29.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]

══ 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 167 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.4530.9843.505
LipidmapsStructureEntry0.3990.0200.432