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This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on kjohnson1

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

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-24 12:42:58 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 12:45:34 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 156.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


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

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-06-24 12:43:49.620][biodb::testContext]
biodb.INFO [2024-06-24 12:43:49.625][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:49.626][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-24 12:43:49.627][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:49.628][biodb::testContext]
biodb.INFO [2024-06-24 12:43:49.637][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:49.639][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:49.649][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:49.650][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:43:49.651][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:43:49.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.655][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:43:49.695][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:43:49.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.699][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:43:49.700][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:43:49.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.703][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:43:49.704][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:43:49.705][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:43:49.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.707][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[2024-06-24 12:43:49.708][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:43:49.708][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:43:49.710][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:43:49.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.714][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:43:49.714][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:43:49.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.717][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:43:49.718][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:43:49.719][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:43:49.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.723][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:43:49.724][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:43:49.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.728][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:43:49.729][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:43:49.730][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:43:49.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.733][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:49.734][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:43:49.735][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:43:49.736][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:43:49.737][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:43:49.737][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:43:49.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.740][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[2024-06-24 12:43:49.740][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:43:49.741][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:43:49.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.744][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:43:49.745][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:43:49.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.747][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[2024-06-24 12:43:49.748][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:43:49.749][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:43:49.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.752][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:43:49.753][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:43:49.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.756][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[2024-06-24 12:43:49.757][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:43:49.757][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:43:49.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.760][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:49.761][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:43:49.776][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:43:49.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.779][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:43:49.780][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:43:49.781][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:43:49.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.788][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:43:49.822][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.837][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:43:49.839][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.839][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:49.840][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.841][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.842][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.843][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.844][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:49.844][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:49.845][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.846][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:43:49.847][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:49.848][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.849][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:49.849][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:49.849][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:49.849][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:49.849][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:49.850][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:49.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:49.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.855][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.856][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:49.857][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:49.858][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.858][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.859][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:43:49.861][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.862][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:49.863][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:49.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.865][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.866][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.867][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.868][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:49.868][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:49.869][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.870][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:43:49.871][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:49.878][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.879][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.880][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:49.880][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:49.880][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:49.880][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:49.880][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:49.881][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:49.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:49.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.886][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:49.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:49.888][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.889][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.890][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:43:49.892][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.893][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:43:49.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.894][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:49.895][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.896][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.897][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.897][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.898][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:49.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:49.900][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.900][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:43:49.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:49.902][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.903][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.904][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.904][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:49.905][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.907][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:49.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.910][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.910][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:49.911][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:49.912][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.913][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.914][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:43:49.915][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.916][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:49.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.918][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:49.918][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.919][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.920][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.922][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:49.922][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:49.923][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.924][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:43:49.925][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:49.925][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.926][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:49.928][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.929][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:49.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:49.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:49.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:49.934][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:49.935][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.936][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:49.937][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:49.937][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:49.938][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:49.944][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:49.944][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.949][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[2024-06-24 12:43:49.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:49.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:49.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:49.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:49.998][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[2024-06-24 12:43:49.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:49.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.008][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[2024-06-24 12:43:50.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.012][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[2024-06-24 12:43:50.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.016][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:43:50.022][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:43:50.024][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:43:50.025][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:43:50.026][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:50.027][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:50.028][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:50.030][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:50.031][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:43:50.032][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:50.033][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:50.034][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:43:50.035][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:50.036][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:50.038][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:43:50.039][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:50.040][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:43:50.041][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:43:50.042][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:50.044][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:43:50.051][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:43:50.053][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:43:50.054][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:43:50.055][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:43:50.056][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:43:50.057][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:43:50.059][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:43:50.060][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:43:50.061][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:43:50.062][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:43:50.063][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:43:50.064][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:43:50.065][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:43:50.067][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:43:50.068][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:43:50.069][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:43:50.071][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:43:50.072][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:43:50.074][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:43:50.075][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:43:50.076][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:43:50.077][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:43:50.079][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:43:50.080][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:43:50.082][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:43:50.083][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:43:50.085][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:43:50.086][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:43:50.087][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:43:50.088][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:43:50.090][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:43:50.091][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:43:50.092][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:43:50.093][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:43:50.094][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:43:50.095][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:43:50.097][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:43:50.098][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:43:50.099][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:43:50.100][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:43:50.101][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:43:50.102][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:43:50.103][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:43:50.105][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:43:50.106][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:43:50.107][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:43:50.108][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:50.109][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:50.111][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:43:50.112][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:43:50.113][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:43:50.114][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:43:50.115][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:43:50.116][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:43:50.118][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:43:50.119][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:43:50.120][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:43:50.121][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:43:50.123][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:43:50.124][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:43:50.125][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:43:50.126][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:43:50.127][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:43:50.133][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:43:50.136][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:50.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:50.141][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.143][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:50.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:50.263][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:50.274][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:43:50.276][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:50.277][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:43:50.279][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:50.280][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:50.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:50.281][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:50.282][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:50.283][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:50.284][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:50.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:50.286][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:50.286][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-24 12:43:50.287][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-24 12:43:50.288][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-24 12:43:50.289][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:50.290][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:50.290][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:50.291][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:50.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:50.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:50.293][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:50.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:50.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:50.296][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:50.297][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-24 12:43:50.297][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-24 12:43:50.299][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:50.300][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:50.301][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:50.302][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:50.309][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-24 12:43:50.311][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:50.343][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:43:50.344][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-24 12:43:50.349][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:43:50.354][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-24 12:43:50.359][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-24 12:43:50.360][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-24 12:43:50.361][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-24 12:43:50.362][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-24 12:43:50.376][biodb::testThat]
biodb.INFO [2024-06-24 12:43:50.377][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-24 12:43:50.378][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:50.379][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:50.384][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-24 12:43:50.386][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:50.391][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-24 12:43:50.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:50.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:50.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:50.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:50.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:50.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:50.421][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.TRACE[2024-06-24 12:43:50.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:50.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:50.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.470][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:50.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:50.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.473][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:50.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:50.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.504][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.511][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.514][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:43:50.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.517][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:43:50.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:50.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:50.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:50.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:50.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.536][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:43:50.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-24 12:43:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.550][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:43:50.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.673][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.676][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.682][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:50.705][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-24 12:43:50.709][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:50.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:50.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.712][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:50.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.715][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:50.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:50.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:50.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:50.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.762][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.802][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.805][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.808][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:50.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.831][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.832][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.858][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.859][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.860][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:50.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:50.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.885][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.886][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.887][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.900][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:50.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:50.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:50.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:50.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:50.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.911][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:50.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:50.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.913][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.915][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:50.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:50.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.948][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.950][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.951][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:50.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.969][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.973][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.976][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.977][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.979][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:50.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:50.992][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:50.993][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:50.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:50.995][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.001][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:51.002][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:51.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.008][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:51.009][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:51.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.011][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.016][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:51.017][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:51.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.019][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.023][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.024][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.031][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:51.032][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:51.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.033][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:51.042][biodb::testThat]
biodb.INFO [2024-06-24 12:43:51.043][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-24 12:43:51.044][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:51.044][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:51.059][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-24 12:43:51.069][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:51.074][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-24 12:43:51.075][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:51.076][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-24 12:43:51.077][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:51.109][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:51.110][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-24 12:43:51.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:51.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:51.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:51.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:51.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:51.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:51.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:51.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:51.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:51.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:51.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:51.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.141][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:51.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:43:51.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.144][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:51.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:51.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.148][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:51.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:51.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.151][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:51.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:43:51.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:51.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:51.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.158][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:51.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:43:51.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.161][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:43:51.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:51.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.164][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:43:51.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:51.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.168][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:51.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:51.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:51.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:51.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.181][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:43:51.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.184][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-24 12:43:51.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.195][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:43:51.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.217][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:51.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:51.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.221][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:51.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:51.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.228][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:51.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:43:51.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:51.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:51.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:51.257][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-24 12:43:51.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-24 12:43:51.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-24 12:43:51.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-24 12:43:51.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-24 12:43:51.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-24 12:43:51.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-24 12:43:51.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:51.276][biodb::testThat]
biodb.INFO [2024-06-24 12:43:51.278][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-24 12:43:51.278][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:51.279][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:51.282][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.285][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:51.287][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-24 12:43:51.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:51.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:51.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:51.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:51.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:51.333][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-24 12:43:51.340][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-24 12:43:51.362][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:51.364][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:51.365][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-24 12:43:51.801][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-24 12:43:52.102][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:52.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-24 12:43:52.119][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-24 12:43:52.122][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-24 12:43:52.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:52.134][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:52.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.147][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:52.156][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.157][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-24 12:43:52.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:52.159][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:52.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:52.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:52.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:52.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:52.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:52.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:52.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:52.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-24 12:43:52.316][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:52.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-24 12:43:52.333][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:52.334][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-24 12:43:52.349][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.350][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-24 12:43:52.351][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:52.352][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:52.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.382][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.385][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:52.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:52.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.389][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:52.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.431][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.435][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:43:52.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:52.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:43:52.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.442][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:52.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:43:52.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:52.451][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.452][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-24 12:43:52.453][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:52.454][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.468][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.469][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-24 12:43:52.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:52.471][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.479][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.480][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-24 12:43:52.481][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:52.481][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:52.486][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-24 12:43:52.781][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-24 12:43:52.878][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.880][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-24 12:43:52.881][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:52.882][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:52.891][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:52.893][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:52.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.894][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.895][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:52.896][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:52.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.898][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:52.900][biodb::testThat]
biodb.INFO [2024-06-24 12:43:52.901][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-24 12:43:52.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:52.903][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:52.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:52.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:52.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:52.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:52.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:52.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:52.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:53.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-24 12:43:53.026][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:53.027][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-24 12:43:53.028][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:53.030][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-24 12:43:53.102][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-24 12:43:53.106][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:53.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-24 12:43:53.109][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:53.110][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-24 12:43:53.127][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:53.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:53.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:53.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:53.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:53.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:53.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:53.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:53.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:53.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:53.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:53.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:53.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:53.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:53.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:53.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:53.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:53.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:53.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:53.172][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-24 12:43:53.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:53.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:53.215][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-24 12:43:56.945][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-24 12:44:01.701][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:44:01.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-24 12:44:01.717][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-24 12:44:03.123][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-24 12:44:03.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:03.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:44:03.130][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-24 12:44:03.428][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-24 12:44:03.721][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:44:03.723][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-24 12:44:03.728][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-24 12:44:03.751][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-24 12:44:03.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:03.756][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:03.757][rule$waitAsNeeded] Wait 0.371932 second(s).
biodb.TRACE[2024-06-24 12:44:04.282][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-06-24 12:44:04.583][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-06-24 12:44:04.887][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:44:04.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-24 12:44:04.893][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-24 12:44:04.910][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:04.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:04.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:04.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:44:04.921][biodb::testThat]
biodb.INFO [2024-06-24 12:44:04.922][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-24 12:44:04.923][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:44:04.924][biodb::testThat]
biodb.TRACE[2024-06-24 12:44:04.927][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:44:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:44:04.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:04.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:04.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:44:04.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:44:04.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:04.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:04.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:04.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:04.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:04.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:04.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:04.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:04.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:04.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:44:04.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:04.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:04.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:04.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:04.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:04.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:04.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:44:04.965][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-24 12:44:04.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:04.970][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:04.971][rule$waitAsNeeded] Wait 0.309803 second(s).
biodb.TRACE[2024-06-24 12:44:05.433][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-24 12:44:10.029][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-24 12:44:14.594][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:44:14.596][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-24 12:44:14.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-24 12:44:16.178][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-24 12:44:16.224][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-24 12:44:16.226][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-24 12:44:16.227][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-24 12:44:16.228][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:44:16.229][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:44:16.230][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-24 12:44:16.231][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:44:16.232][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:44:16.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:16.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:16.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:16.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:16.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:16.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:16.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:44:16.259][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-24 12:44:16.262][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:16.263][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:44:16.265][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-24 12:44:16.596][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-06-24 12:44:16.907][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:44:16.910][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-06-24 12:44:16.914][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-06-24 12:44:16.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:16.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:16.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:16.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:16.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:16.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:16.927][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[2024-06-24 12:44:16.928][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-24 12:44:16.932][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:16.933][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:16.934][rule$waitAsNeeded] Wait 0.330664 second(s).
biodb.TRACE[2024-06-24 12:44:17.416][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-24 12:44:17.698][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-24 12:44:18.017][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:44:18.020][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-24 12:44:18.024][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-24 12:44:18.026][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-24 12:44:18.029][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:44:18.030][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-24 12:44:18.032][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-24 12:44:18.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:18.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:18.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:18.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:18.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:18.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:18.045][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.TRACE[2024-06-24 12:44:18.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:44:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:44:18.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:44:18.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:44:18.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.067][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:44:18.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:44:18.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.071][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:44:18.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:44:18.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.075][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.087][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.091][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:44:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.094][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:44:18.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:44:18.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:44:18.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:44:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:44:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.114][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:44:18.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.118][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-24 12:44:18.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.129][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:44:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.136][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.143][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:44:18.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:18.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:18.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:18.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:18.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:18.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:18.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:18.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:44:18.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:44:18.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.185][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:44:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:44:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.189][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:44:18.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:44:18.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.197][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:44:18.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.224][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.227][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:44:18.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.230][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:44:18.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.234][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:44:18.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:44:18.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:44:18.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.240][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:44:18.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:44:18.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:44:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-24 12:44:18.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:44:18.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.264][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:44:18.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:44:18.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.268][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.271][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.277][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:18.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:18.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:44:18.310][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-24 12:44:18.320][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:44:18.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:18.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:18.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:18.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:18.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:18.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:18.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.338][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.341][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.342][private$selectFields]
biodb.TRACE[2024-06-24 12:44:18.343][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:18.344][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:18.345][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.346][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.347][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.348][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.349][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.350][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.351][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.352][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.353][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.354][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.355][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.357][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:18.358][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.362][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.365][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.379][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-24 12:44:18.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:18.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:18.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:18.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:18.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:18.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:18.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:18.392][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.399][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.400][private$selectFields]
biodb.TRACE[2024-06-24 12:44:18.401][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:18.402][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:18.403][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.404][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.404][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.406][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.407][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.408][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.409][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.410][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.411][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.412][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.412][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.415][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:18.416][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.419][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.422][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.426][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-24 12:44:18.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:18.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:18.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:18.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:18.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:18.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:18.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:18.438][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.442][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.445][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.446][private$selectFields]
biodb.TRACE[2024-06-24 12:44:18.447][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:18.448][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:18.449][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.450][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.451][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.453][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.454][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.455][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.457][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.458][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.459][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:18.460][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.462][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.464][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.465][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:18.466][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.469][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.472][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:18.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.476][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-24 12:44:18.477][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:44:18.478][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:44:18.489][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:18.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:44:18.497][biodb::testThat]
biodb.INFO [2024-06-24 12:44:18.499][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-24 12:44:18.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:44:18.500][biodb::testThat]
biodb.TRACE[2024-06-24 12:44:18.504][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:44:18.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:44:18.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:44:18.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:44:18.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:18.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:44:18.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:18.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:18.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:18.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:18.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:18.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:18.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:44:18.608][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-06-24 12:44:18.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:18.613][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:44:18.615][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-06-24 12:44:22.593][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-06-24 12:44:27.078][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:44:27.084][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-24 12:44:27.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-24 12:44:28.648][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:44:28.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:28.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:28.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:28.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:28.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:28.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:28.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:28.694][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.721][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.722][private$selectFields]
biodb.TRACE[2024-06-24 12:44:28.723][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:28.724][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:28.725][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.726][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.727][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.728][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.729][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.730][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.732][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.743][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.744][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.746][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.748][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:28.749][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.757][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.761][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-24 12:44:28.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:28.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:28.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:28.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:28.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:28.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:28.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:28.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.778][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.781][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.782][private$selectFields]
biodb.TRACE[2024-06-24 12:44:28.783][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:28.784][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:28.785][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.786][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.787][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.788][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.789][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.790][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.792][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.793][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.794][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.795][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.795][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.798][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:28.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.806][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.810][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-24 12:44:28.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:28.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:28.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:28.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:28.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:28.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:28.822][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.TRACE[2024-06-24 12:44:28.823][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.827][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.830][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.831][private$selectFields]
biodb.TRACE[2024-06-24 12:44:28.832][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:28.833][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:28.834][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.835][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.836][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.837][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.838][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.839][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.841][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.841][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.842][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:28.843][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.844][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.846][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.847][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:28.848][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.851][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:28.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.859][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-24 12:44:28.860][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:44:28.861][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:44:28.870][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:28.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:28.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:44:28.879][biodb::testThat]
biodb.INFO [2024-06-24 12:44:28.880][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-24 12:44:28.881][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:44:28.882][biodb::testThat]
biodb.TRACE[2024-06-24 12:44:28.886][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:44:28.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:44:28.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:44:28.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:44:28.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:28.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:28.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:28.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:28.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:28.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:28.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:28.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:29.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:29.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:44:29.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:29.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:44:29.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:29.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:29.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:29.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:29.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:29.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:29.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:44:29.204][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-24 12:44:29.208][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:44:29.209][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-24 12:44:29.210][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:44:29.274][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-24 12:44:30.536][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:44:30.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:30.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:30.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:30.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:30.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:30.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:30.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:30.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.553][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.556][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.557][private$selectFields]
biodb.TRACE[2024-06-24 12:44:30.558][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:30.559][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:30.559][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.560][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.561][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.562][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.563][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.564][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.566][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.567][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.568][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.568][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.569][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.571][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.572][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:30.573][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.576][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.579][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.584][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-24 12:44:30.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:30.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:30.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:30.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:30.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:30.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:30.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:30.596][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.599][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.602][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.603][private$selectFields]
biodb.TRACE[2024-06-24 12:44:30.604][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:30.604][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:30.605][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.606][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.607][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.608][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.609][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.610][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.611][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.612][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.613][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.614][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.614][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.616][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.617][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:30.617][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.621][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.624][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.627][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-24 12:44:30.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:30.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:30.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:30.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:30.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:30.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:30.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:44:30.638][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.642][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.645][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.645][private$selectFields]
biodb.TRACE[2024-06-24 12:44:30.646][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:44:30.647][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:44:30.648][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.648][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.649][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.651][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.652][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.652][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.654][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.655][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.655][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:44:30.656][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.657][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.658][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.659][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-24 12:44:30.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.663][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.666][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:30.670][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-24 12:44:30.670][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:44:30.671][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:44:30.689][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:30.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:44:30.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:30.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:44:30.696][biodb::testThat]
biodb.INFO [2024-06-24 12:44:30.697][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-24 12:44:30.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:44:30.699][biodb::testThat]
biodb.DEBUG[2024-06-24 12:44:30.700][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-24 12:44:30.701][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:44:30.702][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-24 12:44:30.704][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:44:30.704][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:44:30.705][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:44:30.706][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-24 12:44:30.707][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:44:30.708][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:44:30.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:30.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:30.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:30.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:30.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:30.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:30.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:44:30.732][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-24 12:44:30.735][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:30.736][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:44:30.737][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:31.029][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:31.030][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:31.031][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:31.032][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:31.578][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:31.579][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:31.580][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:31.581][rule$waitAsNeeded] Wait 0.156139 second(s).
biodb.TRACE[2024-06-24 12:44:31.889][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:32.250][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:32.251][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:32.252][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:32.253][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:32.721][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:32.722][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:32.723][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:32.724][rule$waitAsNeeded] Wait 0.164408 second(s).
biodb.TRACE[2024-06-24 12:44:32.940][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:33.233][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:33.234][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:33.235][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:33.236][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:33.808][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:33.810][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:33.810][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:33.811][rule$waitAsNeeded] Wait 0.128069 second(s).
biodb.TRACE[2024-06-24 12:44:34.006][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:34.276][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:34.277][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:34.278][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:34.279][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:34.531][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:34.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:34.534][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:34.535][rule$waitAsNeeded] Wait 0.47133 second(s).
biodb.TRACE[2024-06-24 12:44:35.157][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:35.433][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:35.434][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:35.435][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:35.436][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:35.864][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:35.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:35.866][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:35.867][rule$waitAsNeeded] Wait 0.289853 second(s).
biodb.TRACE[2024-06-24 12:44:36.289][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:36.582][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:36.584][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:36.585][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:36.586][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:36.855][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:36.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:36.857][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:36.858][rule$waitAsNeeded] Wait 0.429777 second(s).
biodb.TRACE[2024-06-24 12:44:37.440][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:37.742][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:37.744][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:37.745][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:37.746][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:38.026][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:38.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:38.029][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:38.030][rule$waitAsNeeded] Wait 0.409519 second(s).
biodb.TRACE[2024-06-24 12:44:38.591][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:38.846][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:38.848][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:38.849][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:38.850][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:39.095][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:39.096][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:39.097][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:39.098][rule$waitAsNeeded] Wait 0.492122 second(s).
biodb.TRACE[2024-06-24 12:44:39.607][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:39.847][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:39.878][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:39.879][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:39.880][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:40.115][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:40.116][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:40.117][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:40.118][rule$waitAsNeeded] Wait 0.488153 second(s).
biodb.TRACE[2024-06-24 12:44:40.758][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-24 12:44:40.997][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:40.998][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:40.999][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:41.000][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-24 12:44:41.246][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-24 12:44:41.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-24 12:44:41.250][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:44:41.251][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:44:41.252][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-24 12:44:41.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:41.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:41.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:41.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:41.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:41.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:41.263][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.TRACE[2024-06-24 12:44:41.264][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:41.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:41.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:41.268][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:41.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:44:41.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:41.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:41.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:41.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:41.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:41.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:41.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:41.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:41.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:41.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:41.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:41.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:41.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:41.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:41.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:44:41.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:44:41.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:44:41.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:44:41.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:44:41.290][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-24 12:44:41.290][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-24 12:44:41.299][biodb::testThat]
biodb.INFO [2024-06-24 12:44:41.301][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-24 12:44:41.301][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:44:41.302][biodb::testThat]
biodb.DEBUG[2024-06-24 12:44:41.311][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-24 12:44:41.312][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-24 12:44:41.313][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-24 12:44:41.315][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-24 12:44:41.316][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-24 12:44:41.317][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:44:41.318][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:44:41.319][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-24 12:44:41.320][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:44:41.321][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:44:41.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:41.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:41.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:41.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:41.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:41.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:41.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:44:41.336][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-24 12:44:41.339][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:41.340][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:41.341][rule$waitAsNeeded] Wait 0.416227 second(s).
biodb.TRACE[2024-06-24 12:44:41.909][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:42.147][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:42.148][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:42.149][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:42.150][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:42.395][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:42.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:42.397][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:42.398][rule$waitAsNeeded] Wait 0.510362 second(s).
biodb.TRACE[2024-06-24 12:44:43.060][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:43.308][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:43.309][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:43.310][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:43.311][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:43.546][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:43.547][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:43.548][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:43.549][rule$waitAsNeeded] Wait 0.510143 second(s).
biodb.TRACE[2024-06-24 12:44:44.211][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:44.464][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:44.465][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:44.466][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:44.467][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:44.708][private$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[2024-06-24 12:44:44.710][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:44.710][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:44.712][rule$waitAsNeeded] Wait 0.498935 second(s).
biodb.TRACE[2024-06-24 12:44:45.309][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:45.553][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:45.554][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:45.555][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:45.556][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:45.785][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:45.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:45.787][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:45.788][rule$waitAsNeeded] Wait 0.520712 second(s).
biodb.TRACE[2024-06-24 12:44:46.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:46.601][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:46.602][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:46.603][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:46.604][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:46.846][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:46.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:46.848][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:46.849][rule$waitAsNeeded] Wait 0.503972 second(s).
biodb.TRACE[2024-06-24 12:44:47.431][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:47.672][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:47.673][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:47.674][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:47.674][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:47.920][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:47.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:47.922][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:47.923][rule$waitAsNeeded] Wait 0.508723 second(s).
biodb.TRACE[2024-06-24 12:44:48.436][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:48.681][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:48.682][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:48.683][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:48.684][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:49.188][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:49.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:49.190][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:49.191][rule$waitAsNeeded] Wait 0.244354 second(s).
biodb.TRACE[2024-06-24 12:44:49.587][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:49.797][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:49.798][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:49.799][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:49.800][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:50.043][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:50.044][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:50.044][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:50.045][rule$waitAsNeeded] Wait 0.541229 second(s).
biodb.TRACE[2024-06-24 12:44:50.738][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:50.984][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:50.985][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:50.986][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:50.987][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:51.223][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:51.224][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:51.225][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:51.226][rule$waitAsNeeded] Wait 0.511991 second(s).
biodb.TRACE[2024-06-24 12:44:51.889][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-24 12:44:52.121][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:52.122][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:52.123][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:52.124][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-24 12:44:52.370][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:52.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:44:52.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:44:52.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:44:52.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:44:52.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:44:52.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:44:52.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:44:52.382][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-24 12:44:52.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:52.385][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:52.386][rule$waitAsNeeded] Wait 0.5026 second(s).
biodb.TRACE[2024-06-24 12:44:52.935][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:44:53.192][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:53.193][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:53.194][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:53.195][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:44:53.434][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:53.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:53.436][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:53.437][rule$waitAsNeeded] Wait 0.496877 second(s).
biodb.TRACE[2024-06-24 12:44:53.982][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:44:54.232][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:54.233][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:54.234][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:54.235][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:44:54.473][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:54.474][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:54.475][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:54.477][rule$waitAsNeeded] Wait 0.505162 second(s).
biodb.TRACE[2024-06-24 12:44:55.133][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:44:55.384][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:55.386][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:55.387][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:55.388][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:44:55.628][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:55.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:55.630][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:55.631][rule$waitAsNeeded] Wait 0.502343 second(s).
biodb.TRACE[2024-06-24 12:44:56.285][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:44:56.519][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:56.520][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:56.521][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:56.522][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:44:56.764][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:56.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:56.767][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:56.768][rule$waitAsNeeded] Wait 0.516166 second(s).
biodb.TRACE[2024-06-24 12:44:57.436][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:44:57.679][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:57.680][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:57.681][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:57.682][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:44:58.102][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:58.103][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:58.104][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:58.105][rule$waitAsNeeded] Wait 0.330278 second(s).
biodb.TRACE[2024-06-24 12:44:58.471][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:44:58.713][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:58.714][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:58.715][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:58.716][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:44:58.949][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:44:58.951][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:44:58.952][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:44:58.953][rule$waitAsNeeded] Wait 0.517708 second(s).
biodb.TRACE[2024-06-24 12:44:59.622][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:44:59.875][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:44:59.876][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:44:59.877][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:44:59.878][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:45:00.123][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:45:00.124][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:00.125][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:00.126][rule$waitAsNeeded] Wait 0.495444 second(s).
biodb.TRACE[2024-06-24 12:45:00.773][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:45:01.015][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:45:01.016][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:45:01.017][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:45:01.018][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:45:01.253][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:45:01.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:01.255][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:01.256][rule$waitAsNeeded] Wait 0.516826 second(s).
biodb.TRACE[2024-06-24 12:45:01.924][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:45:02.161][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:45:02.162][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:45:02.163][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:45:02.164][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:45:02.444][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-24 12:45:02.445][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:02.446][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:02.447][rule$waitAsNeeded] Wait 0.476108 second(s).
biodb.TRACE[2024-06-24 12:45:03.075][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-24 12:45:03.308][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-24 12:45:03.309][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-24 12:45:03.310][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-24 12:45:03.311][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-24 12:45:03.523][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-24 12:45:03.526][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-24 12:45:03.528][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:45:03.529][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-24 12:45:03.530][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-24 12:45:03.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:45:03.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:03.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:03.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:03.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:03.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:03.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:45:03.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.545][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:45:03.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:45:03.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:03.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:03.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:03.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:03.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:03.560][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.TRACE[2024-06-24 12:45:03.561][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.564][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:03.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:03.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:03.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:03.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:03.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:45:03.601][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-24 12:45:03.602][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-24 12:45:03.603][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-24 12:45:03.815][biodb::testThat]
biodb.INFO [2024-06-24 12:45:03.816][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-24 12:45:03.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:03.818][biodb::testThat]
biodb.INFO [2024-06-24 12:45:03.864][biodb::testThat]
biodb.INFO [2024-06-24 12:45:03.865][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-24 12:45:03.866][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:03.867][biodb::testThat]
biodb.INFO [2024-06-24 12:45:03.877][biodb::testThat]
biodb.INFO [2024-06-24 12:45:03.878][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-24 12:45:03.879][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:03.880][biodb::testThat]
biodb.DEBUG[2024-06-24 12:45:03.883][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-24 12:45:03.886][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:03.887][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:03.889][rule$waitAsNeeded] Wait 0.185791 second(s).
biodb.TRACE[2024-06-24 12:45:04.227][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-24 12:45:07.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-24 12:45:12.602][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:45:12.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-24 12:45:12.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-24 12:45:13.936][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:13.937][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:13.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:13.939][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:13.940][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:13.941][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:13.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:13.942][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:45:13.944][biodb::testThat]
biodb.INFO [2024-06-24 12:45:13.945][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-24 12:45:13.946][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:13.947][biodb::testThat]
biodb.ERROR[2024-06-24 12:45:13.962][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-24 12:45:13.981][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-24 12:45:13.996][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:45:13.998][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-24 12:45:13.999][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-24 12:45:14.000][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:45:14.001][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.002][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.004][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:45:14.017][biodb::testContext]
biodb.INFO [2024-06-24 12:45:14.018][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:45:14.019][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-24 12:45:14.020][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:45:14.020][biodb::testContext]
biodb.INFO [2024-06-24 12:45:14.023][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:45:14.025][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:45:14.031][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:45:14.032][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:45:14.033][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:45:14.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.036][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:45:14.037][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:45:14.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.040][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:45:14.041][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:45:14.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.044][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:45:14.045][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:45:14.045][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:45:14.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.048][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:45:14.049][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:45:14.050][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:45:14.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.053][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:45:14.054][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:45:14.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.056][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[2024-06-24 12:45:14.057][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:45:14.058][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:45:14.058][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:45:14.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.061][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:45:14.062][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:45:14.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.065][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:45:14.066][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:45:14.068][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:45:14.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.071][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:45:14.072][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:45:14.073][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:45:14.074][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:45:14.075][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:45:14.076][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:45:14.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.079][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:45:14.080][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:45:14.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.083][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:45:14.084][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:45:14.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.087][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:45:14.088][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:45:14.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.092][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:45:14.093][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:45:14.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.096][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[2024-06-24 12:45:14.097][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:45:14.098][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:45:14.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.102][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:45:14.102][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:45:14.118][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:45:14.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.122][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:45:14.123][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:45:14.123][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:45:14.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.127][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:45:14.129][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.129][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:45:14.130][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:14.132][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.134][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.136][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:45:14.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:14.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.138][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:45:14.139][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:14.140][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.141][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.142][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:45:14.142][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:45:14.142][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:45:14.142][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:45:14.142][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:45:14.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:14.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.145][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:14.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.148][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.149][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:14.150][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:14.151][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.151][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.152][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:45:14.154][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.155][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:45:14.156][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.157][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:14.158][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.159][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.159][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.160][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.161][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:45:14.162][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:14.163][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.164][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:45:14.164][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:14.165][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.166][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.167][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:45:14.167][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:45:14.167][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:45:14.167][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:45:14.167][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:45:14.168][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:14.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.170][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.170][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:14.171][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.172][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.173][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.174][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.175][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:14.175][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:14.176][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.177][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.178][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:45:14.180][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.181][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:45:14.182][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.183][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:14.183][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.184][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.185][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.186][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.187][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:45:14.188][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:14.188][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.189][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:45:14.190][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:14.191][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.192][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.193][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.194][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:14.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.196][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:14.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.217][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:14.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:14.220][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.221][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.222][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:45:14.224][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.224][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:45:14.225][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.226][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:14.227][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.228][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.229][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.230][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.230][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:45:14.232][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:14.233][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.234][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:45:14.235][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:14.236][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.236][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.237][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.238][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:14.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.240][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.241][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:14.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.244][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.244][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.245][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:14.246][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:14.247][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.248][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.249][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:45:14.250][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.279][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[2024-06-24 12:45:14.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.297][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[2024-06-24 12:45:14.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.312][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:45:14.313][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:45:14.314][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:45:14.315][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:45:14.316][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:45:14.318][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:45:14.319][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:45:14.320][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:45:14.321][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:45:14.322][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:45:14.323][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:45:14.325][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:45:14.326][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:45:14.327][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:45:14.328][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:45:14.329][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:45:14.331][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:45:14.332][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:45:14.333][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:45:14.334][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:45:14.335][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:45:14.336][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:45:14.338][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:45:14.339][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:45:14.340][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:45:14.341][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:45:14.343][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:45:14.344][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:45:14.345][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:45:14.346][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:45:14.347][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:45:14.349][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:45:14.350][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:45:14.351][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:45:14.352][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:45:14.354][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:45:14.355][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:45:14.356][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:45:14.357][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:45:14.358][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:45:14.359][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:45:14.360][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:45:14.362][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:45:14.363][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:45:14.364][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:45:14.365][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:45:14.366][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:45:14.367][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:45:14.369][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:45:14.370][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:45:14.371][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:45:14.373][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:45:14.374][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:45:14.376][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:45:14.377][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:45:14.378][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:45:14.379][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:45:14.380][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:45:14.382][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:45:14.383][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:45:14.384][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:45:14.385][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:45:14.386][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:45:14.387][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:45:14.389][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:45:14.390][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:45:14.391][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:45:14.392][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:45:14.393][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:45:14.394][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:45:14.395][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:45:14.397][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:45:14.398][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:45:14.399][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:45:14.400][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:45:14.401][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:45:14.402][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:45:14.404][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:45:14.405][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:45:14.406][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:45:14.407][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:45:14.408][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:45:14.409][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:45:14.410][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:45:14.412][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:45:14.413][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:45:14.414][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.415][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.421][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[2024-06-24 12:45:14.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.426][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[2024-06-24 12:45:14.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.431][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[2024-06-24 12:45:14.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.466][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[2024-06-24 12:45:14.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:14.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:14.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:14.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:14.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:14.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:14.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:14.520][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-24 12:45:14.522][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:45:14.524][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.525][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:14.528][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.529][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.531][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:45:14.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:14.533][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.533][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-24 12:45:14.534][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-24 12:45:14.535][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-24 12:45:14.536][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:14.537][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:45:14.537][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:45:14.538][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:14.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.539][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.540][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:14.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:14.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:14.542][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:14.543][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-24 12:45:14.543][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-24 12:45:14.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:14.545][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:14.546][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:14.547][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:14.548][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-24 12:45:14.549][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:45:14.553][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:45:14.554][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-24 12:45:14.556][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:45:14.558][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-24 12:45:14.559][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-24 12:45:14.560][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-24 12:45:14.561][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-24 12:45:14.562][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-24 12:45:14.564][biodb::testThat]
biodb.INFO [2024-06-24 12:45:14.565][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-24 12:45:14.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:14.567][biodb::testThat]
biodb.DEBUG[2024-06-24 12:45:14.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-06-24 12:45:14.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:14.578][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:45:14.580][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-24 12:45:14.878][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-06-24 12:45:15.187][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:45:15.190][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-24 12:45:15.194][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-24 12:45:15.203][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-06-24 12:45:15.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:15.207][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:15.209][rule$waitAsNeeded] Wait 0.370401 second(s).
biodb.TRACE[2024-06-24 12:45:15.716][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-24 12:45:16.045][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-24 12:45:16.354][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:45:16.357][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-24 12:45:16.361][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-24 12:45:16.371][biodb::testThat]
biodb.INFO [2024-06-24 12:45:16.372][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-24 12:45:16.373][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:16.374][biodb::testThat]
biodb.INFO [2024-06-24 12:45:16.406][biodb::testThat]
biodb.INFO [2024-06-24 12:45:16.407][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-24 12:45:16.408][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:16.409][biodb::testThat]
biodb.DEBUG[2024-06-24 12:45:16.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-24 12:45:16.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:16.417][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:16.418][rule$waitAsNeeded] Wait 0.296793 second(s).
biodb.TRACE[2024-06-24 12:45:16.867][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-24 12:45:17.018][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-24 12:45:17.162][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:45:17.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-24 12:45:17.168][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-24 12:45:17.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-24 12:45:17.177][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:45:17.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-24 12:45:17.180][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:45:17.181][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-24 12:45:17.187][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-06-24 12:45:17.190][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:17.191][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:17.192][rule$waitAsNeeded] Wait 0.673656 second(s).
biodb.TRACE[2024-06-24 12:45:17.887][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-24 12:45:18.050][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-24 12:45:18.202][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:45:18.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-24 12:45:18.209][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-24 12:45:18.216][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-06-24 12:45:18.219][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:18.220][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:45:18.221][rule$waitAsNeeded] Wait 0.66477 second(s).
biodb.TRACE[2024-06-24 12:45:19.038][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-24 12:45:19.926][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-24 12:45:20.989][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:45:20.992][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-24 12:45:20.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-24 12:45:21.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-06-24 12:45:21.190][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:45:21.191][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:45:21.193][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-24 12:45:22.107][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-24 12:45:23.194][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:45:23.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-24 12:45:23.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-24 12:45:23.416][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:45:23.418][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-24 12:45:23.419][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-24 12:45:23.420][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:45:23.421][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.422][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.423][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:45:23.429][biodb::testContext]
biodb.INFO [2024-06-24 12:45:23.430][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:45:23.431][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-24 12:45:23.432][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:45:23.432][biodb::testContext]
biodb.INFO [2024-06-24 12:45:23.435][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:45:23.436][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:45:23.441][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:45:23.442][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:45:23.443][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:45:23.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.446][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:45:23.447][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:45:23.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.450][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:45:23.450][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:45:23.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.453][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:45:23.454][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:45:23.455][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:45:23.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.458][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:45:23.458][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:45:23.459][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:45:23.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.462][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:45:23.463][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:45:23.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.466][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:45:23.466][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:45:23.467][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:45:23.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.470][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:45:23.471][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:45:23.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.474][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:45:23.475][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:45:23.475][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:45:23.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.478][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:45:23.479][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:45:23.480][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:45:23.481][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:45:23.481][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:45:23.482][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:45:23.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.485][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:45:23.486][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:45:23.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.489][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:45:23.489][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:45:23.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.492][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:45:23.493][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:45:23.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.496][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:45:23.497][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:45:23.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.499][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:45:23.500][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:45:23.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.503][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:45:23.504][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:45:23.520][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:45:23.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.524][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:45:23.525][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:45:23.525][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:45:23.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.529][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:45:23.531][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.531][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:45:23.532][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.533][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:23.534][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.536][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.536][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.537][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:45:23.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:23.539][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.540][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:45:23.540][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:23.541][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.542][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.543][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:45:23.543][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:45:23.543][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:45:23.543][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:45:23.543][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:45:23.544][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:23.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.546][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:23.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.549][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.549][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.550][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:23.551][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:23.552][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.553][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.554][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:45:23.555][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.556][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:45:23.557][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:23.559][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.560][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.561][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.563][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:45:23.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:23.565][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.566][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:45:23.567][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:23.568][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.569][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.570][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:45:23.570][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:45:23.570][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:45:23.570][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:45:23.570][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:45:23.571][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:23.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.573][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:23.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.575][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.576][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.578][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.578][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:23.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:23.580][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.581][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.582][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:45:23.584][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.585][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:45:23.586][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.587][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:23.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.590][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.591][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.592][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:45:23.593][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:23.594][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.594][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:45:23.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:23.596][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.597][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.598][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.599][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:23.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:23.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.604][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:23.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:23.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.607][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.608][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:45:23.610][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.611][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:45:23.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.614][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:23.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.617][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.618][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.619][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:45:23.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:23.621][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.622][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:45:23.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:23.624][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.625][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.626][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.626][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:23.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.629][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:23.630][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.632][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.633][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:23.634][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:23.635][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.636][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.637][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:45:23.638][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.653][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[2024-06-24 12:45:23.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.676][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[2024-06-24 12:45:23.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.679][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[2024-06-24 12:45:23.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.683][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[2024-06-24 12:45:23.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.689][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[2024-06-24 12:45:23.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.693][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[2024-06-24 12:45:23.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.696][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[2024-06-24 12:45:23.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.707][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[2024-06-24 12:45:23.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.714][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:45:23.715][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:45:23.717][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:45:23.718][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:45:23.719][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:45:23.720][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:45:23.721][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:45:23.722][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:45:23.723][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:45:23.725][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:45:23.726][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:45:23.727][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:45:23.728][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:45:23.729][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:45:23.730][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:45:23.731][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:45:23.732][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:45:23.734][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:45:23.735][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:45:23.736][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:45:23.737][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:45:23.738][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:45:23.739][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:45:23.740][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:45:23.742][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:45:23.743][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:45:23.744][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:45:23.745][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:45:23.746][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:45:23.747][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:45:23.748][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:45:23.749][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:45:23.751][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:45:23.752][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:45:23.753][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:45:23.754][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:45:23.755][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:45:23.756][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:45:23.757][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:45:23.758][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:45:23.760][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:45:23.761][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:45:23.762][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:45:23.763][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:45:23.764][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:45:23.765][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:45:23.766][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:45:23.768][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:45:23.769][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:45:23.770][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:45:23.771][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:45:23.772][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:45:23.773][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:45:23.775][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:45:23.776][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:45:23.777][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:45:23.778][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:45:23.779][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:45:23.780][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:45:23.782][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:45:23.783][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:45:23.784][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:45:23.785][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:45:23.786][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:45:23.787][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:45:23.789][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:45:23.790][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:45:23.791][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:45:23.792][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:45:23.793][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:45:23.794][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:45:23.796][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:45:23.797][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:45:23.798][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:45:23.799][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:45:23.800][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:45:23.802][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:45:23.803][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:45:23.804][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:45:23.805][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:45:23.806][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:45:23.807][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:45:23.809][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:45:23.810][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:45:23.812][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:45:23.814][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:45:23.814][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.816][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.900][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[2024-06-24 12:45:23.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:45:23.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:23.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:23.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:23.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:23.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:23.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:45:23.925][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-24 12:45:23.927][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:45:23.929][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.930][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:45:23.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.934][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.935][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.936][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.936][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:45:23.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:45:23.938][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.939][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-24 12:45:23.940][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-24 12:45:23.941][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:45:23.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:45:23.942][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:45:23.943][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:45:23.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.945][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:45:23.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:45:23.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:45:23.948][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:45:23.948][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-24 12:45:23.948][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-24 12:45:23.949][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:45:23.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:45:23.951][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:45:23.952][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:45:23.953][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-24 12:45:23.954][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:45:23.958][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:45:23.959][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-24 12:45:23.960][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-24 12:45:23.961][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-24 12:45:23.962][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-24 12:45:23.963][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-24 12:45:23.964][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-24 12:45:23.965][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-24 12:45:23.967][biodb::testThat]
biodb.INFO [2024-06-24 12:45:23.968][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-24 12:45:23.969][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:45:23.969][biodb::testThat]
biodb.DEBUG[2024-06-24 12:45:23.973][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-24 12:45:23.977][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:45:23.978][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-24 12:45:23.979][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:45:24.042][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-24 12:45:25.597][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-24 12:45:25.599][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-24 12:45:25.601][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-24 12:45:25.602][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-24 12:45:25.604][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-24 12:45:25.605][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:45:25.606][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-24 12:45:25.607][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-24 12:45:25.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:45:25.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:25.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:25.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:25.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:25.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:25.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:45:25.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.638][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:45:25.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:45:25.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.641][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:45:25.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:45:25.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.644][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.651][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.654][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.657][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:45:25.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.661][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:45:25.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:25.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:25.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.667][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:25.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:25.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.678][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:45:25.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.681][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-24 12:45:25.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.691][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:45:25.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.711][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.714][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.721][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:45:25.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:45:25.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:25.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:25.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:25.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:25.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:25.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:45:25.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.762][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:45:25.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-24 12:45:25.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.766][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:45:25.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:45:25.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.769][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.775][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.782][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:45:25.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.785][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-24 12:45:25.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:25.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:25.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.791][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:25.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:25.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.802][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:45:25.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.805][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-24 12:45:25.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.816][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-24 12:45:25.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.824][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.867][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:45:25.899][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-06-24 12:45:25.902][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:45:25.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:45:25.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:25.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:25.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:25.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:25.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:25.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:45:25.915][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:45:25.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:45:25.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:45:25.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:45:25.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:45:25.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:45:25.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.925][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:45:25.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:45:25.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.929][private$selectFields] Fields none
biodb.TRACE[2024-06-24 12:45:25.930][private$selectFields]
biodb.TRACE[2024-06-24 12:45:25.931][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-24 12:45:25.932][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:45:25.933][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:45:25.934][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.936][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.938][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.939][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.940][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.941][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.942][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.943][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.944][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.945][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.946][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.948][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.948][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.949][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.951][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.952][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:25.953][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:25.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.955][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.956][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.957][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.958][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.959][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.961][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.964][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.965][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.967][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.968][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.968][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.971][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.972][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:25.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:25.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.976][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.977][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:25.978][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:25.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.981][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:25.982][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:25.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.984][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.984][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.985][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:25.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.988][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.989][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:45:25.990][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:45:25.990][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:25.991][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:25.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:25.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.996][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:25.997][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.998][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:25.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:25.999][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.000][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.001][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.003][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.004][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.006][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.007][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.010][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.011][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.013][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.014][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.014][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.016][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.017][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-24 12:45:26.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.038][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.041][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.044][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.047][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.073][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.086][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.090][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.114][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-06-24 12:45:26.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:45:26.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:26.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:26.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:26.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:26.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:26.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:45:26.127][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:45:26.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:45:26.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.131][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:45:26.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:45:26.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.134][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:45:26.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:45:26.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.137][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:45:26.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:45:26.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.140][private$selectFields] Fields none
biodb.TRACE[2024-06-24 12:45:26.141][private$selectFields]
biodb.TRACE[2024-06-24 12:45:26.142][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-24 12:45:26.143][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:45:26.143][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:45:26.144][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.145][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.146][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.147][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.148][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.150][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.150][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.151][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.153][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.153][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.154][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.156][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.159][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.159][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.160][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.162][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.163][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.163][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.165][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.165][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.166][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.168][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.168][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.169][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.172][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.173][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.175][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.177][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.178][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.179][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.181][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.182][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.184][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.184][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.185][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.187][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.188][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.190][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.191][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.191][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.193][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.194][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.194][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.196][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.197][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:45:26.198][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-24 12:45:26.198][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.199][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.203][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.204][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.206][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.207][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.207][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.211][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.212][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.214][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.215][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.216][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.219][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.219][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.221][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.222][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.223][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.224][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.225][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.226][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.227][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.228][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-24 12:45:26.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:45:26.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:45:26.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:45:26.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.252][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.256][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.259][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-24 12:45:26.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.266][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-24 12:45:26.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:45:26.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.282][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.288][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:45:26.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:45:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:45:26.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:45:26.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.304][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.307][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.314][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-24 12:45:26.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:45:26.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:45:26.325][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-06-24 12:45:26.326][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:45:26.327][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-24 12:45:26.334][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:45:26.336][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-24 12:45:26.337][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-24 12:45:26.338][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:45:26.339][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:45:26.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:45:26.341][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:45:26.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:45:26.342][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:45:26.343][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".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]

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

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

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

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

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.2850.6403.616
LipidmapsStructureEntry0.4180.0140.434