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This page was generated on 2024-06-11 14:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on lconway

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

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-09 19:01:36 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 19:06:55 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 319.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


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

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-06-09 19:02:32.693][biodb::testContext]
biodb.INFO [2024-06-09 19:02:32.697][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-09 19:02:32.698][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-09 19:02:32.699][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-09 19:02:32.700][biodb::testContext]
biodb.INFO [2024-06-09 19:02:32.707][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-09 19:02:32.710][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-09 19:02:32.721][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:02:32.723][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-09 19:02:32.724][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-09 19:02:32.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.729][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-09 19:02:32.767][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-09 19:02:32.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.773][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-09 19:02:32.774][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-09 19:02:32.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.778][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-09 19:02:32.779][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-09 19:02:32.781][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-09 19:02:32.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.785][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-09 19:02:32.786][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-09 19:02:32.788][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-09 19:02:32.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.792][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-09 19:02:32.794][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-09 19:02:32.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.798][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-09 19:02:32.799][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-09 19:02:32.800][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-09 19:02:32.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.805][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-09 19:02:32.806][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-09 19:02:32.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.811][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-09 19:02:32.813][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-09 19:02:32.814][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-09 19:02:32.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.818][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-09 19:02:32.820][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-09 19:02:32.821][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-09 19:02:32.822][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-09 19:02:32.823][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-09 19:02:32.825][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-09 19:02:32.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.829][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-09 19:02:32.830][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-09 19:02:32.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.834][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-09 19:02:32.835][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-09 19:02:32.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.839][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-09 19:02:32.840][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-09 19:02:32.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.844][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-09 19:02:32.845][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-09 19:02:32.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.850][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-09 19:02:32.852][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-09 19:02:32.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.855][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-09 19:02:32.857][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-09 19:02:32.879][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-09 19:02:32.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.885][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-09 19:02:32.886][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-09 19:02:32.887][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-09 19:02:32.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:32.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:32.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:32.893][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-09 19:02:32.933][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:32.953][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-09 19:02:32.954][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:32.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:02:32.956][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:32.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:02:32.958][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:32.959][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:02:32.960][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:02:32.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:02:32.961][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:32.963][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-09 19:02:32.964][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:02:32.965][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:32.966][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:32.968][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:02:32.968][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:02:32.968][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-09 19:02:32.968][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-09 19:02:32.968][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-09 19:02:32.969][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:02:32.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:32.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:32.972][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:02:32.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:32.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:32.976][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:02:32.977][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:32.978][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:02:32.979][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:02:32.980][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:32.981][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:32.983][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-09 19:02:32.985][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:32.986][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-09 19:02:32.988][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:32.989][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:02:32.990][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:32.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:02:32.991][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:32.992][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:02:32.994][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-09 19:02:32.995][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:02:32.997][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:32.998][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-09 19:02:33.000][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:02:33.001][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.003][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.011][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:02:33.011][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:02:33.011][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-09 19:02:33.011][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-09 19:02:33.011][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-09 19:02:33.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:02:33.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:02:33.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.022][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:02:33.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:02:33.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.027][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.029][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-09 19:02:33.031][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.033][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-09 19:02:33.034][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.035][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:02:33.036][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.037][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.038][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.039][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.040][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:02:33.042][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:02:33.043][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.044][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-09 19:02:33.045][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:02:33.047][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.048][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.048][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.049][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:02:33.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:02:33.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.054][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.055][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.056][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:02:33.057][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:02:33.057][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.059][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.060][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-09 19:02:33.063][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.064][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-09 19:02:33.065][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.067][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:02:33.068][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.069][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.070][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.071][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.072][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-09 19:02:33.072][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:02:33.073][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.074][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-09 19:02:33.075][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:02:33.076][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.077][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.077][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:02:33.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.082][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:02:33.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.086][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.087][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.087][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:02:33.088][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:02:33.089][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.090][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.094][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:02:33.095][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.126][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[2024-06-09 19:02:33.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.143][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[2024-06-09 19:02:33.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.153][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[2024-06-09 19:02:33.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.187][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-09 19:02:33.192][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-09 19:02:33.194][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-09 19:02:33.195][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-09 19:02:33.197][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-09 19:02:33.199][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-09 19:02:33.201][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-09 19:02:33.202][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-09 19:02:33.204][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-09 19:02:33.205][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-09 19:02:33.206][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-09 19:02:33.207][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-09 19:02:33.208][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-09 19:02:33.210][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-09 19:02:33.211][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-09 19:02:33.212][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-09 19:02:33.213][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-09 19:02:33.214][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-09 19:02:33.215][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-09 19:02:33.217][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-09 19:02:33.218][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-09 19:02:33.219][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-09 19:02:33.225][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-09 19:02:33.227][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-09 19:02:33.228][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-09 19:02:33.229][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-09 19:02:33.231][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-09 19:02:33.232][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-09 19:02:33.234][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-09 19:02:33.235][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-09 19:02:33.236][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-09 19:02:33.238][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-09 19:02:33.239][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-09 19:02:33.240][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-09 19:02:33.242][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-09 19:02:33.243][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-09 19:02:33.245][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-09 19:02:33.247][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-09 19:02:33.249][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-09 19:02:33.251][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-09 19:02:33.253][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-09 19:02:33.254][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-09 19:02:33.256][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-09 19:02:33.258][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-09 19:02:33.259][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-09 19:02:33.261][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-09 19:02:33.262][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-09 19:02:33.264][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-09 19:02:33.266][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-09 19:02:33.268][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-09 19:02:33.269][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-09 19:02:33.271][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-09 19:02:33.272][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-09 19:02:33.274][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-09 19:02:33.275][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-09 19:02:33.276][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-09 19:02:33.277][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-09 19:02:33.278][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-09 19:02:33.280][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-09 19:02:33.281][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-09 19:02:33.282][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-09 19:02:33.283][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-09 19:02:33.284][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-09 19:02:33.286][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-09 19:02:33.287][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-09 19:02:33.288][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-09 19:02:33.289][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-09 19:02:33.290][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-09 19:02:33.291][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-09 19:02:33.293][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-09 19:02:33.294][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-09 19:02:33.295][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-09 19:02:33.296][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-09 19:02:33.297][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-09 19:02:33.299][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-09 19:02:33.300][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-09 19:02:33.301][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-09 19:02:33.302][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-09 19:02:33.303][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-09 19:02:33.305][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-09 19:02:33.306][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-09 19:02:33.307][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-09 19:02:33.308][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-09 19:02:33.313][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-09 19:02:33.315][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-09 19:02:33.318][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:02:33.319][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.320][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.426][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[2024-06-09 19:02:33.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:02:33.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:33.436][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-09 19:02:33.446][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:02:33.449][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.451][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.452][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.454][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:02:33.456][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.459][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.460][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.461][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:02:33.463][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:02:33.464][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.464][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-09 19:02:33.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-09 19:02:33.466][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-09 19:02:33.467][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-09 19:02:33.469][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:02:33.469][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:02:33.470][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:02:33.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:02:33.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:02:33.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:02:33.476][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:02:33.477][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-09 19:02:33.477][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-09 19:02:33.478][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:02:33.478][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:02:33.479][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-09 19:02:33.480][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:02:33.488][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-09 19:02:33.490][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-09 19:02:33.517][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:02:33.518][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-09 19:02:33.524][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:02:33.528][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-09 19:02:33.533][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-09 19:02:33.535][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-09 19:02:33.537][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-09 19:02:33.538][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-09 19:02:33.549][biodb::testThat]
biodb.INFO [2024-06-09 19:02:33.550][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-09 19:02:33.552][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:33.553][biodb::testThat]
biodb.TRACE[2024-06-09 19:02:33.568][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-09 19:02:33.570][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-09 19:02:33.575][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-09 19:02:33.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:02:33.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:33.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:33.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:33.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:33.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:33.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:02:33.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:02:33.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:02:33.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.663][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:02:33.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:02:33.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:02:33.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:02:33.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.686][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:33.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:33.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:33.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:33.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.722][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:33.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:33.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:33.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:33.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.733][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:02:33.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:33.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.738][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:02:33.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:33.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.743][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:33.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.748][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:33.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:33.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.766][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:02:33.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.770][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-09 19:02:33.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.791][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:02:33.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:33.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.921][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:33.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:33.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:33.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:33.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:02:33.968][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-09 19:02:33.971][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:02:33.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:02:33.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:02:33.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:02:33.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.978][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-09 19:02:33.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-09 19:02:33.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:33.982][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-09 19:02:33.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-09 19:02:33.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:33.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.078][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.081][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.085][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:34.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.117][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.118][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.120][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:34.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:34.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:34.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:34.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:34.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:34.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.151][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:34.152][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:34.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:34.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:34.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.170][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.176][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.181][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.186][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.187][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:34.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:34.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.210][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:34.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:34.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:34.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:34.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.221][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:34.223][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:34.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.225][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:34.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:34.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.262][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.263][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.265][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.287][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.298][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.303][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.304][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.306][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.307][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.324][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:34.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:34.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.327][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.335][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.337][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:34.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.340][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.351][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:34.353][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:34.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:34.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.368][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.376][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:34.378][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:34.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.381][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:34.393][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.395][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:34.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:34.398][ef$get] fields variable is a list.
biodb.INFO [2024-06-09 19:02:34.414][biodb::testThat]
biodb.INFO [2024-06-09 19:02:34.415][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-09 19:02:34.416][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:34.417][biodb::testThat]
biodb.DEBUG[2024-06-09 19:02:34.436][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-09 19:02:34.447][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-09 19:02:34.452][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.INFO [2024-06-09 19:02:34.454][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-06-09 19:02:34.456][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-09 19:02:34.457][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-09 19:02:34.459][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-09 19:02:34.461][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-09 19:02:34.462][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-09 19:02:34.463][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-09 19:02:34.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:02:34.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:34.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:34.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:34.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:34.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:34.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:02:34.488][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-06-09 19:02:34.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:02:34.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:02:34.522][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-09 19:02:35.900][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2024-06-09 19:02:36.502][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:02:36.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2024-06-09 19:02:36.521][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2024-06-09 19:02:36.542][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2024-06-09 19:02:36.545][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-09 19:02:36.573][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-09 19:02:36.575][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-09 19:02:36.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:02:36.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:02:36.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:02:36.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:02:36.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:02:36.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:02:36.590][FUN] Functions in observer BiodbConfig: [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[2024-06-09 19:02:36.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:02:36.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:02:36.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:02:36.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:02:36.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:02:36.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:02:36.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.621][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:02:36.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:02:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.625][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:36.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:36.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.628][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:36.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:02:36.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.632][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:36.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:36.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.635][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:36.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:02:36.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.639][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:02:36.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:36.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.642][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:02:36.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:36.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.646][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:36.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:36.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:02:36.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:02:36.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.660][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:02:36.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.669][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-09 19:02:36.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.679][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:02:36.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.708][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:36.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:36.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:36.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:36.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.723][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:36.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:02:36.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:02:36.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:02:36.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:02:36.758][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-09 19:02:36.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-09 19:02:36.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-09 19:02:36.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-09 19:02:36.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-09 19:02:36.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-09 19:02:36.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-09 19:02:36.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-09 19:02:36.782][biodb::testThat]
biodb.INFO [2024-06-09 19:02:36.784][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-09 19:02:36.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:36.787][biodb::testThat]
biodb.TRACE[2024-06-09 19:02:36.790][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.791][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.793][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:02:36.795][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-09 19:02:36.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:36.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:36.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:36.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:36.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:02:36.856][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-09 19:02:36.887][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-09 19:02:36.922][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:02:36.923][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:02:36.942][private$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[2024-06-09 19:02:37.521][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[2024-06-09 19:02:38.376][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:02:38.379][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-09 19:02:38.394][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-09 19:02:38.396][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-09 19:02:38.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:38.418][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:38.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.421][ef$get] fields variable is a list.
biodb.INFO [2024-06-09 19:02:38.426][biodb::testThat]
biodb.INFO [2024-06-09 19:02:38.427][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-09 19:02:38.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:38.429][biodb::testThat]
biodb.TRACE[2024-06-09 19:02:38.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:38.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:38.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:38.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:38.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:38.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:38.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:02:38.579][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[2024-06-09 19:02:38.582][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-09 19:02:38.596][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-09 19:02:38.597][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-09 19:02:38.599][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-09 19:02:38.626][biodb::testThat]
biodb.INFO [2024-06-09 19:02:38.627][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-09 19:02:38.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:38.629][biodb::testThat]
biodb.TRACE[2024-06-09 19:02:38.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.676][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-09 19:02:38.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-09 19:02:38.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-09 19:02:38.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-09 19:02:38.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.740][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.746][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:02:38.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.752][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-09 19:02:38.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-09 19:02:38.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:38.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-09 19:02:38.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-09 19:02:38.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:38.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-09 19:02:38.774][biodb::testThat]
biodb.INFO [2024-06-09 19:02:38.775][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-09 19:02:38.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:38.778][biodb::testThat]
biodb.INFO [2024-06-09 19:02:38.790][biodb::testThat]
biodb.INFO [2024-06-09 19:02:38.792][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-09 19:02:38.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:38.793][biodb::testThat]
biodb.INFO [2024-06-09 19:02:38.804][biodb::testThat]
biodb.INFO [2024-06-09 19:02:38.805][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-09 19:02:38.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:38.814][biodb::testThat]
biodb.DEBUG[2024-06-09 19:02:38.819][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-09 19:02:39.531][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-09 19:02:39.913][biodb::testThat]
biodb.INFO [2024-06-09 19:02:39.914][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-09 19:02:39.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:39.917][biodb::testThat]
biodb.TRACE[2024-06-09 19:02:39.926][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:39.928][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:39.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:39.930][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:39.931][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:39.932][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:39.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:39.934][ef$get] fields variable is a list.
biodb.INFO [2024-06-09 19:02:39.936][biodb::testThat]
biodb.INFO [2024-06-09 19:02:39.937][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-09 19:02:39.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:02:39.939][biodb::testThat]
biodb.TRACE[2024-06-09 19:02:39.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:39.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:39.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:39.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:39.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:39.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:39.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:39.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:02:39.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:02:39.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:39.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:02:40.054][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[2024-06-09 19:02:40.058][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-09 19:02:40.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-09 19:02:40.063][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-09 19:02:40.067][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-09 19:02:40.143][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[2024-06-09 19:02:40.146][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-09 19:02:40.153][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-09 19:02:40.154][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-09 19:02:40.156][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-09 19:02:40.178][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-09 19:02:40.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-09 19:02:40.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:40.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:40.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-09 19:02:40.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-09 19:02:40.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:40.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:40.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:40.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:40.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:40.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:40.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:40.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:40.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:40.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:02:40.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:02:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:02:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:02:40.238][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[2024-06-09 19:02:40.242][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:02:40.244][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:02:40.247][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-09 19:02:44.288][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-09 19:02:56.297][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:02:56.300][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-09 19:02:56.414][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-09 19:02:59.151][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-09 19:02:59.174][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:02:59.176][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:02:59.184][private$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[2024-06-09 19:02:59.801][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&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-09 19:03:00.641][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:03:00.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-09 19:03:00.651][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-09 19:03:00.695][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[2024-06-09 19:03:00.701][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:00.703][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:00.706][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-06-09 19:03:01.330][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-06-09 19:03:01.923][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:03:01.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-09 19:03:01.934][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-09 19:03:01.976][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:01.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:01.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:01.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-09 19:03:02.003][biodb::testThat]
biodb.INFO [2024-06-09 19:03:02.005][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-09 19:03:02.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:03:02.010][biodb::testThat]
biodb.TRACE[2024-06-09 19:03:02.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-09 19:03:02.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-09 19:03:02.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:02.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:02.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-09 19:03:02.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-09 19:03:02.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:02.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:02.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:02.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:02.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:02.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:02.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:02.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:02.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:02.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:03:02.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:02.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:02.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:02.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:02.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:02.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:02.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:03:02.092][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-09 19:03:02.098][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:02.100][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:02.104][private$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[2024-06-09 19:03:06.285][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[2024-06-09 19:03:19.529][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:03:19.534][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-09 19:03:19.670][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-09 19:03:22.580][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-09 19:03:22.672][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-09 19:03:22.675][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-09 19:03:22.677][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-09 19:03:22.678][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-09 19:03:22.679][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-09 19:03:22.680][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-09 19:03:22.681][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-09 19:03:22.682][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-09 19:03:22.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:22.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:22.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:22.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:22.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:22.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:22.731][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[2024-06-09 19:03:22.733][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-09 19:03:22.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:22.770][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:22.782][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-09 19:03:23.475][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-06-09 19:03:24.130][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:03:24.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-06-09 19:03:24.222][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-06-09 19:03:24.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:24.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:24.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:24.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:24.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:24.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:24.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:03:24.493][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-09 19:03:24.538][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:24.542][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:24.552][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-09 19:03:25.256][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-09 19:03:25.924][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:03:25.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-09 19:03:25.965][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-09 19:03:26.029][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-09 19:03:26.090][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-09 19:03:26.092][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-09 19:03:26.104][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-09 19:03:26.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:26.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:26.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:26.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:26.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:26.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:26.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:03:26.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:26.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:26.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:26.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:26.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:03:26.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:03:26.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:03:26.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:03:26.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.656][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:03:26.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:03:26.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.715][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:03:26.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:03:26.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.760][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:26.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:26.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.915][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:26.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:26.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:26.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:26.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.107][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.144][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:03:27.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:27.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.189][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:03:27.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:27.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:03:27.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:03:27.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.232][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:03:27.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:03:27.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.302][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:03:27.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.336][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-09 19:03:27.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.358][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:03:27.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.365][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.392][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.425][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:03:27.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:27.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:27.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:27.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:27.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:27.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:27.537][FUN] Functions in observer BiodbConfig: [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[2024-06-09 19:03:27.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:03:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:03:27.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.641][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:03:27.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:03:27.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.663][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:03:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:03:27.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.669][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:27.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:27.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:27.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:03:27.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.684][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:03:27.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.704][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:03:27.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:27.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.708][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:03:27.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:03:27.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:03:27.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.716][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:03:27.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:03:27.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.732][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:03:27.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.740][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-09 19:03:27.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:03:27.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.769][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:03:27.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:03:27.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.779][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.786][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:03:27.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:03:27.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:03:27.865][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-09 19:03:27.874][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-09 19:03:27.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:27.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:27.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:27.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:27.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:27.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:27.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:03:27.889][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.923][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:27.925][private$selectFields]
biodb.TRACE[2024-06-09 19:03:27.926][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:27.927][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:27.929][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:27.930][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.931][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.933][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.935][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.936][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.938][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.940][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:27.941][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:27.942][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.944][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.946][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:27.947][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.972][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-09 19:03:27.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:27.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:27.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:27.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:27.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:27.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:27.988][FUN] Functions in observer BiodbConfig: [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[2024-06-09 19:03:27.989][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:27.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:27.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:27.997][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:27.998][private$selectFields]
biodb.TRACE[2024-06-09 19:03:28.000][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:28.001][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:28.003][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:28.004][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.005][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.009][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.010][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.013][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.014][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:28.015][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:28.016][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.017][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.019][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.020][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.024][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.032][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.038][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-09 19:03:28.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:28.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:28.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:28.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:28.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:28.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:28.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:03:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.073][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.079][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:28.080][private$selectFields]
biodb.TRACE[2024-06-09 19:03:28.081][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:28.082][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:28.083][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:28.083][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.084][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.113][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.115][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.117][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.119][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.121][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:28.123][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:28.124][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.125][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.128][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.129][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:28.130][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.135][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:28.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.156][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-09 19:03:28.157][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-09 19:03:28.158][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-09 19:03:28.223][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:28.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:28.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-09 19:03:28.235][biodb::testThat]
biodb.INFO [2024-06-09 19:03:28.236][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-09 19:03:28.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:03:28.237][biodb::testThat]
biodb.TRACE[2024-06-09 19:03:28.240][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-09 19:03:28.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-09 19:03:28.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-09 19:03:28.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-09 19:03:28.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:28.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:28.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:28.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:03:28.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:28.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:28.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:28.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:28.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:28.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:28.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:03:28.341][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-06-09 19:03:28.345][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:28.347][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:28.350][private$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[2024-06-09 19:03:32.385][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[2024-06-09 19:03:44.143][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:03:44.166][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-09 19:03:44.302][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-09 19:03:45.832][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-09 19:03:45.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:45.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:45.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:45.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:45.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:45.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:45.877][FUN] Functions in observer BiodbConfig: [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[2024-06-09 19:03:45.892][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.899][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.935][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:45.937][private$selectFields]
biodb.TRACE[2024-06-09 19:03:45.938][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:45.940][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:45.941][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:45.943][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.945][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.947][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.949][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.950][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.953][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.954][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:45.969][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:45.971][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.973][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.975][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.977][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:45.978][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.984][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:45.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:45.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:45.997][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-09 19:03:45.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:45.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:46.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:46.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:46.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:46.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:46.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:03:46.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.023][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.029][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.030][private$selectFields]
biodb.TRACE[2024-06-09 19:03:46.032][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:46.033][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:46.035][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.036][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.038][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.040][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.042][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.043][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.046][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.047][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.048][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.050][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.051][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.053][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.054][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:46.056][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.067][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.073][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-09 19:03:46.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:46.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:46.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:46.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:46.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:46.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:46.087][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.TRACE[2024-06-09 19:03:46.088][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.100][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.101][private$selectFields]
biodb.TRACE[2024-06-09 19:03:46.102][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:46.104][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:46.105][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.106][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.107][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.110][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.111][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.113][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.116][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.118][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.120][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:46.121][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.123][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.125][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.127][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:46.128][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.133][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.138][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:46.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.144][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-09 19:03:46.145][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-09 19:03:46.146][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-09 19:03:46.159][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:46.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:46.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-09 19:03:46.171][biodb::testThat]
biodb.INFO [2024-06-09 19:03:46.173][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-09 19:03:46.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:03:46.176][biodb::testThat]
biodb.TRACE[2024-06-09 19:03:46.180][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-09 19:03:46.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-09 19:03:46.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-09 19:03:46.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-09 19:03:46.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:46.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:03:46.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:46.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:03:46.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:46.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:46.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:46.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:46.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:46.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:46.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:03:46.274][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[2024-06-09 19:03:46.278][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-09 19:03:46.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-09 19:03:46.281][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-09 19:03:46.333][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-09 19:03:47.799][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-09 19:03:47.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:47.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:47.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:47.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:47.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:47.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:47.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:03:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.838][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.871][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:47.873][private$selectFields]
biodb.TRACE[2024-06-09 19:03:47.884][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:47.886][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:47.888][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:47.889][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.891][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.900][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.902][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.905][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.906][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:47.915][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:47.917][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.919][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.923][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:47.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.956][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:47.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:47.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:47.963][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-09 19:03:47.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:47.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:47.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:47.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:47.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:47.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:47.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:03:48.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.008][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.022][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.023][private$selectFields]
biodb.TRACE[2024-06-09 19:03:48.025][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:48.026][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:48.034][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.036][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.038][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.057][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.059][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.060][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.063][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.065][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.071][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.072][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.074][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.077][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.079][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:48.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.115][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-09 19:03:48.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:48.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:48.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:48.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:48.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:48.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:48.134][FUN] Functions in observer BiodbConfig: [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[2024-06-09 19:03:48.136][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.177][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.180][private$selectFields]
biodb.TRACE[2024-06-09 19:03:48.181][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-09 19:03:48.183][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:03:48.184][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.185][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.187][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.199][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.201][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.203][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.206][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.218][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.220][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:03:48.223][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.226][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.237][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.239][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-09 19:03:48.242][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.303][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.318][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:03:48.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:03:48.328][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-09 19:03:48.329][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-09 19:03:48.344][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-09 19:03:48.388][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:48.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-09 19:03:48.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:03:48.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-09 19:03:48.414][biodb::testThat]
biodb.INFO [2024-06-09 19:03:48.416][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-09 19:03:48.417][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:03:48.419][biodb::testThat]
biodb.DEBUG[2024-06-09 19:03:48.430][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-09 19:03:48.432][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-09 19:03:48.435][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-09 19:03:48.437][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-09 19:03:48.439][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-09 19:03:48.447][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-09 19:03:48.449][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-09 19:03:48.451][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-09 19:03:48.453][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-09 19:03:48.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:03:48.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:03:48.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:03:48.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:03:48.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:03:48.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:03:48.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:03:48.516][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-09 19:03:48.521][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:48.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:48.531][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:49.108][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:49.125][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:49.127][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[2024-06-09 19:03:49.128][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:49.738][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:49.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:49.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:49.742][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:50.329][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:50.330][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:50.331][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[2024-06-09 19:03:50.332][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:50.943][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:50.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:50.945][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:50.946][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:51.537][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:51.538][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:51.539][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[2024-06-09 19:03:51.540][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:52.401][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:52.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:52.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:52.404][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:52.986][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:52.989][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:52.990][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[2024-06-09 19:03:52.992][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:53.780][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:53.781][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:53.782][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:53.783][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:54.340][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:54.344][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:54.345][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[2024-06-09 19:03:54.346][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:54.915][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:54.916][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:54.918][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:54.920][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:55.556][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:55.557][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:55.559][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[2024-06-09 19:03:55.561][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:56.342][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:56.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:56.346][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:56.347][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:56.943][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:56.944][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:56.946][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[2024-06-09 19:03:56.948][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:57.477][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:57.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:57.482][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:57.484][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:58.010][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:58.011][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:58.013][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[2024-06-09 19:03:58.014][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:58.564][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:58.565][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:58.566][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:58.568][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:03:59.120][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:03:59.121][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:03:59.122][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[2024-06-09 19:03:59.123][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:03:59.656][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:03:59.666][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:03:59.668][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:03:59.670][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-09 19:04:00.202][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:00.203][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:00.204][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[2024-06-09 19:04:00.205][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-09 19:04:00.729][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-09 19:04:00.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-09 19:04:00.733][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-09 19:04:00.734][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-09 19:04:00.735][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-09 19:04:00.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:04:00.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:04:00.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:04:00.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:04:00.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:04:00.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:04:00.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:04:00.789][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:00.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:00.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:00.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:00.792][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:00.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:00.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:00.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:01.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:01.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:01.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:01.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:01.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:01.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:01.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:01.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:01.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:01.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:01.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:01.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:01.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:01.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:01.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:01.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:01.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:01.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:01.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:01.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:01.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:01.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:01.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:01.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:04:01.554][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-09 19:04:01.555][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-09 19:04:01.638][biodb::testThat]
biodb.INFO [2024-06-09 19:04:01.639][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-09 19:04:01.640][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:04:01.641][biodb::testThat]
biodb.DEBUG[2024-06-09 19:04:01.749][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-09 19:04:01.752][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-09 19:04:01.767][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-09 19:04:01.864][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-09 19:04:01.884][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-09 19:04:01.885][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-09 19:04:01.886][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-09 19:04:01.887][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-09 19:04:01.889][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-09 19:04:01.890][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-09 19:04:01.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:04:01.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:04:01.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:04:02.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:04:02.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:04:02.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:04:02.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:04:02.257][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-09 19:04:02.400][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:02.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:02.404][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:02.930][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:02.931][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:02.931][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:02.943][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:03.758][private$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[2024-06-09 19:04:03.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:03.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:03.762][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:04.287][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:04.290][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:04.293][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:04.410][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:05.011][private$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[2024-06-09 19:04:05.130][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:05.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:05.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:05.708][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:05.710][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:05.863][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:06.165][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:06.765][private$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[2024-06-09 19:04:06.768][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:06.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:06.936][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:07.482][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:07.530][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:07.579][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:07.747][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:08.743][private$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[2024-06-09 19:04:08.752][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:08.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:08.770][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:09.389][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:09.433][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:09.557][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:09.659][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:10.271][private$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[2024-06-09 19:04:10.334][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:10.358][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:10.394][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:11.009][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:11.067][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:11.211][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:11.285][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:12.365][private$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[2024-06-09 19:04:12.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:12.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:12.525][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:13.177][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:13.178][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:13.190][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:13.229][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:14.028][private$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[2024-06-09 19:04:17.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:17.048][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:17.050][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:17.615][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:17.639][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:17.640][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:17.641][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:18.148][private$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[2024-06-09 19:04:18.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:18.184][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:18.185][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:18.740][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:18.787][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:18.789][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:18.791][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:19.345][private$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[2024-06-09 19:04:19.346][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:19.347][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:19.349][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-09 19:04:19.889][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:19.890][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:19.891][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-09 19:04:19.892][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-09 19:04:20.692][private$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[2024-06-09 19:04:20.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:04:20.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:04:20.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:04:20.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:04:20.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:04:20.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:04:20.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:04:20.875][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-09 19:04:20.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:20.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:20.976][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:21.529][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:21.531][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:21.533][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[2024-06-09 19:04:21.566][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:22.098][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:22.107][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:22.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:22.109][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:22.631][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:22.632][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:22.633][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[2024-06-09 19:04:22.633][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:23.434][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:23.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:23.436][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:23.437][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:23.966][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:23.968][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:23.971][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[2024-06-09 19:04:23.973][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:24.615][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:24.616][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:24.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:24.630][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:25.177][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:25.178][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:25.179][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[2024-06-09 19:04:25.181][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:25.707][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:25.711][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:25.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:25.721][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:26.252][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:26.255][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:26.262][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[2024-06-09 19:04:26.268][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:26.902][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:27.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:27.156][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:27.231][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:27.834][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:27.837][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:27.842][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[2024-06-09 19:04:27.844][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:28.408][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:28.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:28.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:28.413][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:28.966][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:28.968][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:28.970][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[2024-06-09 19:04:28.971][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:29.489][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:29.490][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:29.491][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:29.492][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:30.027][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:30.034][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:30.039][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[2024-06-09 19:04:30.040][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:30.612][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:30.614][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:30.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:30.617][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:31.143][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:31.145][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:31.146][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[2024-06-09 19:04:31.147][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:31.701][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-09 19:04:31.703][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:31.704][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:31.706][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-09 19:04:32.229][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-09 19:04:32.246][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-09 19:04:32.260][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[2024-06-09 19:04:32.273][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-09 19:04:33.098][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-09 19:04:33.117][private$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[2024-06-09 19:04:33.127][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-09 19:04:33.129][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-09 19:04:33.134][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-09 19:04:33.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:04:33.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:04:33.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:04:33.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:04:33.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:04:33.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:04:33.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:04:33.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.165][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:04:33.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:04:33.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:04:33.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:04:33.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:04:33.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:04:33.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:04:33.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:04:33.202][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.209][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:04:33.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:04:33.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:04:33.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:04:33.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:04:33.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:04:33.717][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-09 19:04:33.719][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-09 19:04:33.721][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-09 19:04:36.409][biodb::testThat]
biodb.INFO [2024-06-09 19:04:36.411][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-09 19:04:36.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:04:36.414][biodb::testThat]
biodb.INFO [2024-06-09 19:04:36.528][biodb::testThat]
biodb.INFO [2024-06-09 19:04:36.529][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-09 19:04:36.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:04:36.532][biodb::testThat]
biodb.INFO [2024-06-09 19:04:36.554][biodb::testThat]
biodb.INFO [2024-06-09 19:04:36.556][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-09 19:04:36.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:04:36.559][biodb::testThat]
biodb.DEBUG[2024-06-09 19:04:36.564][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-09 19:04:36.568][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:04:36.570][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:04:36.591][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-09 19:04:40.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-09 19:05:03.413][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:05:03.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-09 19:05:03.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-09 19:05:18.275][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:05:18.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:05:18.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:05:18.301][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:05:18.302][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:05:18.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:05:18.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:05:18.307][ef$get] fields variable is a list.
biodb.INFO [2024-06-09 19:05:18.331][biodb::testThat]
biodb.INFO [2024-06-09 19:05:18.333][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-09 19:05:18.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:05:18.334][biodb::testThat]
biodb.ERROR[2024-06-09 19:05:18.369][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-09 19:05:18.458][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-09 19:05:18.477][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-09 19:05:18.478][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-09 19:05:18.479][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-09 19:05:18.480][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-09 19:05:18.481][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:18.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:18.482][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:18.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:18.484][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.485][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.INFO [2024-06-09 19:05:18.603][biodb::testContext]
biodb.INFO [2024-06-09 19:05:18.604][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-09 19:05:18.605][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-09 19:05:18.606][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-09 19:05:18.607][biodb::testContext]
biodb.INFO [2024-06-09 19:05:18.690][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-09 19:05:18.692][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-09 19:05:18.771][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:05:18.773][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-09 19:05:18.774][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-09 19:05:18.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.777][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-09 19:05:18.778][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-09 19:05:18.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.794][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-09 19:05:18.796][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-09 19:05:18.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.813][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-09 19:05:18.814][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-09 19:05:18.815][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-09 19:05:18.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.817][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[2024-06-09 19:05:18.818][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-09 19:05:18.819][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-09 19:05:18.820][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-09 19:05:18.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.823][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-09 19:05:18.824][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-09 19:05:18.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.827][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-09 19:05:18.827][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-09 19:05:18.828][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-09 19:05:18.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.831][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-09 19:05:18.832][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-09 19:05:18.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.847][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-09 19:05:18.847][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-09 19:05:18.848][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-09 19:05:18.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.854][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-09 19:05:18.856][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-09 19:05:18.857][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-09 19:05:18.858][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-09 19:05:18.869][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-09 19:05:18.870][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-09 19:05:18.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.873][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-09 19:05:18.874][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-09 19:05:18.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.878][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-09 19:05:18.879][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-09 19:05:18.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.882][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-09 19:05:18.882][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-09 19:05:18.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.887][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-09 19:05:18.912][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-09 19:05:18.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.938][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-09 19:05:18.939][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-09 19:05:18.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:18.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:18.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:18.966][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-09 19:05:18.970][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-09 19:05:19.370][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-09 19:05:19.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:19.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:19.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:19.384][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-09 19:05:19.387][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-09 19:05:19.388][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-09 19:05:19.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:19.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:19.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:19.395][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-09 19:05:19.482][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:19.490][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-09 19:05:19.492][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.536][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:19.570][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.571][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:19.572][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:19.573][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:19.574][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:05:19.576][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:19.577][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.594][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-09 19:05:19.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:19.596][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:19.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.600][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:05:19.600][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:05:19.600][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-09 19:05:19.600][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-09 19:05:19.600][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-09 19:05:19.600][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:19.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:19.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:19.633][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:19.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:19.669][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:19.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:19.692][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:19.693][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:19.706][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:19.718][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:19.719][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:19.720][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-09 19:05:19.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:19.735][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-09 19:05:19.760][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.761][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:19.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.764][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:19.765][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:19.766][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:19.767][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-09 19:05:19.814][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:19.815][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.841][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-09 19:05:19.842][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:19.843][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:19.844][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:19.845][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:05:19.845][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:05:19.845][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-09 19:05:19.845][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-09 19:05:19.845][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-09 19:05:19.846][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:19.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:19.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:19.885][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:19.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:19.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:19.913][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:19.982][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.072][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:20.073][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:20.074][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:20.075][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.076][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-09 19:05:20.091][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.092][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-09 19:05:20.093][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:20.095][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:20.097][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:20.120][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:20.124][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:05:20.125][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:20.126][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:20.127][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-09 19:05:20.128][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:20.129][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.130][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.143][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.239][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:20.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:20.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:20.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:20.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:20.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:20.537][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:20.539][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.540][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:20.540][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:20.541][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:20.542][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.543][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-09 19:05:20.545][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.546][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-09 19:05:20.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.551][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:20.555][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.568][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:20.569][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:20.570][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:20.570][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-09 19:05:20.571][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:20.572][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:20.573][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-09 19:05:20.574][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:20.574][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.575][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:20.576][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.577][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:20.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:20.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:20.579][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:20.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:20.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:20.582][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:20.583][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.583][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:20.585][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:20.586][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:20.587][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:20.592][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:05:20.593][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.683][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[2024-06-09 19:05:20.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.703][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[2024-06-09 19:05:20.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.756][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[2024-06-09 19:05:20.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.760][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[2024-06-09 19:05:20.760][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-09 19:05:20.762][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-09 19:05:20.763][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-09 19:05:20.775][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-09 19:05:20.777][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-09 19:05:20.778][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-09 19:05:20.780][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-09 19:05:20.781][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-09 19:05:20.782][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-09 19:05:20.783][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-09 19:05:20.784][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-09 19:05:20.785][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-09 19:05:20.786][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-09 19:05:20.788][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-09 19:05:20.789][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-09 19:05:20.790][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-09 19:05:20.791][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-09 19:05:20.792][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-09 19:05:20.793][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-09 19:05:20.794][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-09 19:05:20.796][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-09 19:05:20.807][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-09 19:05:20.808][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-09 19:05:20.810][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-09 19:05:20.811][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-09 19:05:20.812][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-09 19:05:20.813][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-09 19:05:20.815][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-09 19:05:20.816][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-09 19:05:20.817][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-09 19:05:20.845][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-09 19:05:20.846][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-09 19:05:20.847][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-09 19:05:20.849][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-09 19:05:20.850][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-09 19:05:20.853][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-09 19:05:20.856][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-09 19:05:20.859][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-09 19:05:20.860][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-09 19:05:20.874][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-09 19:05:20.875][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-09 19:05:20.876][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-09 19:05:20.877][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-09 19:05:20.879][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-09 19:05:20.880][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-09 19:05:20.881][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-09 19:05:20.882][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-09 19:05:20.883][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-09 19:05:20.885][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-09 19:05:20.887][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-09 19:05:20.888][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-09 19:05:20.889][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-09 19:05:20.891][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-09 19:05:20.892][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-09 19:05:20.893][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-09 19:05:20.894][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-09 19:05:20.895][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-09 19:05:20.897][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-09 19:05:20.898][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-09 19:05:20.899][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-09 19:05:20.900][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-09 19:05:20.901][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-09 19:05:20.903][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-09 19:05:20.904][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-09 19:05:20.906][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-09 19:05:20.907][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-09 19:05:20.908][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-09 19:05:20.909][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-09 19:05:20.910][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-09 19:05:20.912][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-09 19:05:20.913][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-09 19:05:20.915][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-09 19:05:20.916][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-09 19:05:20.918][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-09 19:05:20.930][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-09 19:05:20.931][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-09 19:05:20.932][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-09 19:05:20.933][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-09 19:05:20.935][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-09 19:05:20.936][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-09 19:05:20.937][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-09 19:05:20.940][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-09 19:05:20.941][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-09 19:05:20.942][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-09 19:05:20.944][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-09 19:05:20.945][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:05:20.946][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.947][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:20.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:20.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:20.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:20.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:20.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:20.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:20.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:20.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:20.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:20.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:20.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.189][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[2024-06-09 19:05:21.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.194][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[2024-06-09 19:05:21.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.201][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[2024-06-09 19:05:21.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.286][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[2024-06-09 19:05:21.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:21.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:21.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:21.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:21.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:21.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:21.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:21.344][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-09 19:05:21.352][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:05:21.355][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:21.356][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-09 19:05:21.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:21.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:21.358][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:21.359][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:21.360][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:21.361][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:21.361][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:05:21.362][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:21.363][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:21.365][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-09 19:05:21.365][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-09 19:05:21.366][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-09 19:05:21.367][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:21.368][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:05:21.368][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:05:21.369][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:21.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:21.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:21.371][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:21.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:21.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:21.374][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:21.374][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-09 19:05:21.374][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-09 19:05:21.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:21.376][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:21.377][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:21.378][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:21.379][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-09 19:05:21.380][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-09 19:05:21.384][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:05:21.384][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-09 19:05:21.385][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:05:21.387][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-09 19:05:21.389][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-09 19:05:21.390][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-09 19:05:21.391][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-09 19:05:21.392][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-09 19:05:21.393][biodb::testThat]
biodb.INFO [2024-06-09 19:05:21.394][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-09 19:05:21.394][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:05:21.395][biodb::testThat]
biodb.DEBUG[2024-06-09 19:05:21.400][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[2024-06-09 19:05:21.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:05:21.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:05:21.444][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-09 19:05:22.335][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-06-09 19:05:22.922][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:05:22.924][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-09 19:05:23.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-09 19:05:23.231][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-06-09 19:05:23.234][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:05:23.235][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:05:23.237][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-09 19:05:23.828][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[2024-06-09 19:05:24.425][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:05:24.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-09 19:05:24.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-09 19:05:24.448][biodb::testThat]
biodb.INFO [2024-06-09 19:05:24.449][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-09 19:05:24.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:05:24.451][biodb::testThat]
biodb.INFO [2024-06-09 19:05:24.583][biodb::testThat]
biodb.INFO [2024-06-09 19:05:24.584][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-09 19:05:24.585][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:05:24.586][biodb::testThat]
biodb.DEBUG[2024-06-09 19:05:24.589][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[2024-06-09 19:05:24.591][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:05:24.592][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:05:24.594][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-09 19:05:25.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-09 19:05:25.723][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:05:25.733][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-09 19:05:25.737][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-09 19:05:25.744][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-09 19:05:25.748][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-09 19:05:25.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-09 19:05:25.751][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-09 19:05:25.752][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-09 19:05:25.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-06-09 19:05:25.762][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:05:25.763][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:05:25.764][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-09 19:05:26.181][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[2024-06-09 19:05:26.642][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:05:26.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-09 19:05:26.679][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-09 19:05:26.689][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[2024-06-09 19:05:26.702][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:05:26.704][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-09 19:05:26.705][rule$waitAsNeeded] Wait 0.0589938 second(s).
biodb.TRACE[2024-06-09 19:05:26.941][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-09 19:05:28.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-09 19:05:32.494][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:05:32.496][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-09 19:05:32.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-09 19:05:34.474][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[2024-06-09 19:05:34.480][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-09 19:05:34.481][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-09 19:05:34.482][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-09 19:05:35.653][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-09 19:05:40.438][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-09 19:05:40.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-09 19:05:40.497][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-09 19:05:41.504][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-09 19:05:41.507][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-09 19:05:41.509][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-09 19:05:41.510][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-09 19:05:41.512][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:41.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:41.515][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:41.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:41.518][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-09 19:05:41.550][biodb::testContext]
biodb.INFO [2024-06-09 19:05:41.552][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-09 19:05:41.554][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-09 19:05:41.556][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-09 19:05:41.558][biodb::testContext]
biodb.INFO [2024-06-09 19:05:41.566][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-09 19:05:41.570][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-09 19:05:41.590][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:05:41.592][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-09 19:05:41.594][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-09 19:05:41.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.601][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-09 19:05:41.602][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-09 19:05:41.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.608][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-09 19:05:41.610][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-09 19:05:41.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.615][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-09 19:05:41.616][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-09 19:05:41.618][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-09 19:05:41.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.623][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-09 19:05:41.625][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-09 19:05:41.627][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-09 19:05:41.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.633][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-09 19:05:41.635][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-09 19:05:41.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.701][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-09 19:05:41.726][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-09 19:05:41.748][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-09 19:05:41.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.822][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[2024-06-09 19:05:41.899][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-09 19:05:41.910][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-09 19:05:41.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.955][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-09 19:05:41.961][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-09 19:05:41.976][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-09 19:05:41.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:41.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:41.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:41.998][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-09 19:05:42.000][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-09 19:05:42.002][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-09 19:05:42.006][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-09 19:05:42.019][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-09 19:05:42.023][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-09 19:05:42.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:42.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:42.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:42.065][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-09 19:05:42.071][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-09 19:05:42.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:42.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:42.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:42.096][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-09 19:05:42.103][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-09 19:05:42.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:42.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:42.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:42.348][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-09 19:05:42.443][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-09 19:05:42.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:42.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:42.523][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[2024-06-09 19:05:42.528][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-09 19:05:42.673][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-09 19:05:42.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:42.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:43.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:43.379][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-09 19:05:43.613][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-09 19:05:43.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:43.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:43.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:44.021][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-09 19:05:44.091][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-09 19:05:44.291][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-09 19:05:44.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:44.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:44.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:44.639][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-09 19:05:44.751][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-09 19:05:44.794][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-09 19:05:44.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:45.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:45.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:45.377][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-09 19:05:45.619][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:45.713][self$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[2024-06-09 19:05:45.773][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:45.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:45.839][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:45.989][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:46.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:46.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:46.039][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:05:46.051][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:46.259][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:46.313][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-09 19:05:46.316][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:46.349][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:46.353][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:46.386][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:05:46.386][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:05:46.386][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-09 19:05:46.386][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-09 19:05:46.386][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-09 19:05:46.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:46.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:46.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:46.415][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:46.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:46.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:46.704][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:47.130][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:47.400][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:47.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:47.418][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:47.571][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:47.606][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-09 19:05:47.708][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:47.711][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-09 19:05:47.732][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:47.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:47.755][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:47.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:47.779][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:47.781][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:47.783][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-09 19:05:47.787][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:47.793][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:47.797][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-09 19:05:47.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:47.803][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:47.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:47.819][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:05:47.819][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:05:47.819][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-09 19:05:47.819][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-09 19:05:47.819][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-09 19:05:47.882][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:47.892][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:47.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:47.919][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:47.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:47.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:48.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:48.016][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:48.019][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:48.021][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:48.068][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:48.143][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:48.147][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-09 19:05:48.287][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:48.402][self$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[2024-06-09 19:05:48.404][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:48.406][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:48.410][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:48.413][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:48.417][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:48.448][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:48.557][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:05:48.561][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:48.563][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:48.587][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-09 19:05:48.589][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:48.651][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:48.689][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:48.692][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:48.706][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:48.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:48.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:48.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:48.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:48.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:48.901][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:48.924][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:48.926][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:48.929][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:48.931][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:48.943][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:48.966][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-09 19:05:49.056][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:49.058][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-09 19:05:49.059][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:49.061][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:49.062][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:49.081][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:49.084][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:49.086][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:49.090][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-09 19:05:49.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:49.172][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:49.219][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-09 19:05:49.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:49.304][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:49.363][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:49.365][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:49.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:49.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:49.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:49.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:50.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:50.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:50.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:50.348][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:50.460][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:50.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:54.814][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:55.216][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:55.248][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:05:55.269][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:55.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:55.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:55.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:55.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:55.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:55.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:55.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:55.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:55.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:55.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:55.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:55.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:55.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:55.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:55.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:55.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:55.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.204][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[2024-06-09 19:05:56.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.215][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[2024-06-09 19:05:56.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.225][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[2024-06-09 19:05:56.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.240][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-09 19:05:56.251][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-09 19:05:56.255][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-09 19:05:56.258][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-09 19:05:56.262][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-09 19:05:56.266][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-09 19:05:56.269][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-09 19:05:56.274][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-09 19:05:56.276][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-09 19:05:56.278][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-09 19:05:56.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-09 19:05:56.281][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-09 19:05:56.288][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-09 19:05:56.290][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-09 19:05:56.291][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-09 19:05:56.292][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-09 19:05:56.295][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-09 19:05:56.299][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-09 19:05:56.305][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-09 19:05:56.306][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-09 19:05:56.308][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-09 19:05:56.309][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-09 19:05:56.311][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-09 19:05:56.315][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-09 19:05:56.317][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-09 19:05:56.320][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-09 19:05:56.322][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-09 19:05:56.325][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-09 19:05:56.327][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-09 19:05:56.328][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-09 19:05:56.331][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-09 19:05:56.332][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-09 19:05:56.335][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-09 19:05:56.339][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-09 19:05:56.342][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-09 19:05:56.344][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-09 19:05:56.346][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-09 19:05:56.348][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-09 19:05:56.350][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-09 19:05:56.352][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-09 19:05:56.354][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-09 19:05:56.356][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-09 19:05:56.359][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-09 19:05:56.371][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-09 19:05:56.377][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-09 19:05:56.381][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-09 19:05:56.384][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-09 19:05:56.387][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-09 19:05:56.389][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-09 19:05:56.392][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-09 19:05:56.396][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-09 19:05:56.402][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-09 19:05:56.414][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-09 19:05:56.417][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-09 19:05:56.422][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-09 19:05:56.425][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-09 19:05:56.428][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-09 19:05:56.430][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-09 19:05:56.433][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-09 19:05:56.438][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-09 19:05:56.441][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-09 19:05:56.446][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-09 19:05:56.448][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-09 19:05:56.452][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-09 19:05:56.454][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-09 19:05:56.457][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-09 19:05:56.460][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-09 19:05:56.462][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-09 19:05:56.465][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-09 19:05:56.468][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-09 19:05:56.471][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-09 19:05:56.473][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-09 19:05:56.479][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-09 19:05:56.482][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-09 19:05:56.486][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-09 19:05:56.488][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-09 19:05:56.490][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-09 19:05:56.494][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-09 19:05:56.497][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-09 19:05:56.501][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-09 19:05:56.504][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-09 19:05:56.507][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-09 19:05:56.510][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-09 19:05:56.513][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-09 19:05:56.536][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-09 19:05:56.583][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-09 19:05:56.596][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.613][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.676][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[2024-06-09 19:05:56.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.686][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[2024-06-09 19:05:56.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.722][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[2024-06-09 19:05:56.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.918][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[2024-06-09 19:05:56.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-09 19:05:56.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:05:56.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:05:56.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:05:56.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:05:56.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:05:56.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-09 19:05:56.944][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-09 19:05:56.952][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:05:56.955][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:56.958][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-09 19:05:56.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:56.961][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-09 19:05:56.962][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:56.964][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-09 19:05:56.966][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:56.967][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-09 19:05:56.968][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-09 19:05:56.970][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-09 19:05:56.971][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:56.972][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-09 19:05:56.974][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-09 19:05:56.976][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-09 19:05:56.979][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-09 19:05:56.980][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-09 19:05:56.980][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-09 19:05:56.981][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-09 19:05:56.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:56.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:56.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-09 19:05:56.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-09 19:05:56.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-09 19:05:56.991][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-09 19:05:56.994][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-09 19:05:56.994][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-09 19:05:56.996][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-09 19:05:56.997][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-09 19:05:56.998][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-09 19:05:57.000][self$setPropertyValue]
biodb.DEBUG[2024-06-09 19:05:57.003][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-09 19:05:57.004][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-09 19:05:57.077][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:05:57.079][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-09 19:05:57.083][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-09 19:05:57.087][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-09 19:05:57.094][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-09 19:05:57.095][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-09 19:05:57.097][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-09 19:05:57.099][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-09 19:05:57.101][biodb::testThat]
biodb.INFO [2024-06-09 19:05:57.102][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-09 19:05:57.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-09 19:05:57.106][biodb::testThat]
biodb.DEBUG[2024-06-09 19:05:57.118][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-09 19:05:57.124][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-09 19:05:57.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-09 19:05:57.133][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-09 19:05:57.440][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-09 19:06:16.395][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-09 19:06:16.557][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-09 19:06:16.694][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-09 19:06:16.759][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-09 19:06:16.868][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-09 19:06:16.910][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-09 19:06:16.980][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-09 19:06:17.018][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-09 19:06:17.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:06:17.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:06:17.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:06:17.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:06:17.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:06:17.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:06:17.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:06:17.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:17.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:18.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:18.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:18.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:18.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:19.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:19.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:19.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:19.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:19.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:19.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:19.807][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:06:19.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:06:19.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:19.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:19.914][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:06:19.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:06:19.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:19.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.022][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:20.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:20.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.115][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:20.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:20.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:20.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:20.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:20.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.542][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:06:20.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:20.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:06:20.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:20.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:20.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:20.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:20.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:20.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:20.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:20.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:20.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:20.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:20.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:20.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.038][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:06:21.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.074][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-09 19:06:21.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:21.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:21.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.265][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:06:21.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.319][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:21.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:21.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:21.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:21.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:21.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.526][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:21.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:21.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.556][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:21.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:21.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:21.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:21.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:21.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:21.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:21.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:21.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:21.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:23.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:23.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:23.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:23.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:23.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:06:23.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:06:23.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:06:23.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:06:23.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:06:23.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:06:23.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:06:23.445][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.TRACE[2024-06-09 19:06:23.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:23.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:23.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:23.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:23.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:23.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:23.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:23.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:23.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.593][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:06:23.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-09 19:06:23.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.610][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:06:23.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-09 19:06:23.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:23.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:23.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.648][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:23.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:23.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:23.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:23.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:23.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:23.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.693][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:06:23.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:23.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.709][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-09 19:06:23.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:23.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.728][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:23.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:23.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:23.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:23.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:23.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:23.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:24.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:24.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.464][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:06:24.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.515][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-09 19:06:24.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:24.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:24.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.586][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-09 19:06:24.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.621][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.656][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-09 19:06:24.732][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-06-09 19:06:24.744][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-09 19:06:24.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:06:24.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:06:24.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:06:24.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:06:24.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:06:24.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:06:24.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-09 19:06:24.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:06:24.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:06:24.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:06:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:06:24.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-09 19:06:24.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-09 19:06:24.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-09 19:06:24.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-09 19:06:24.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.816][private$selectFields] Fields none
biodb.TRACE[2024-06-09 19:06:24.818][private$selectFields]
biodb.TRACE[2024-06-09 19:06:24.820][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-09 19:06:24.821][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:06:24.823][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:06:24.825][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.826][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.830][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.831][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:24.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:24.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.836][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.838][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:24.839][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:24.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.842][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.844][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:24.846][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:24.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:24.867][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:24.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.884][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:24.889][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:24.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.894][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:24.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:24.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.901][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.902][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.904][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:24.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.922][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:24.924][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:24.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.929][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.944][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:24.945][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:24.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.948][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.951][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:24.955][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:24.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.959][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.962][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:24.964][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:24.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:24.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:24.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.971][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.973][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:24.975][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:24.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:24.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:24.996][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.009][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.012][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.014][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.075][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.118][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.207][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:06:25.208][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:06:25.209][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.210][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.211][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.219][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.220][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.223][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.225][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.227][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.228][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.230][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.230][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.231][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.233][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.234][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.235][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.237][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.237][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.241][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.242][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.243][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.245][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.246][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-09 19:06:25.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.279][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.301][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.309][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.345][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.360][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.382][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.402][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.492][private$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[2024-06-09 19:06:25.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-09 19:06:25.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:06:25.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:06:25.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:06:25.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:06:25.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:06:25.573][FUN] Functions in observer BiodbConfig: [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[2024-06-09 19:06:25.578][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:06:25.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:06:25.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.594][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-09 19:06:25.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-09 19:06:25.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.598][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-09 19:06:25.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-09 19:06:25.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-09 19:06:25.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-09 19:06:25.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.606][private$selectFields] Fields none
biodb.TRACE[2024-06-09 19:06:25.607][private$selectFields]
biodb.TRACE[2024-06-09 19:06:25.608][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-09 19:06:25.609][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-09 19:06:25.610][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:06:25.611][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.625][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.626][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.629][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.630][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.631][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.633][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.635][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.636][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.638][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.639][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.640][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.642][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.643][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.656][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.659][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.661][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.662][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.674][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.674][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.675][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.677][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.678][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.679][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.680][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.681][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.682][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.685][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.686][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.687][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.689][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.690][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.691][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.704][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.707][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.709][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.712][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.713][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.715][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.719][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.719][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.724][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.725][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.726][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.728][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.729][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:06:25.733][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-09 19:06:25.734][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.735][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.745][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.746][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.747][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.779][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.781][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.783][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.785][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.786][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.789][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.791][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.792][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.793][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.795][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.796][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.797][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.808][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.809][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.810][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.812][ef$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.812][private$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[2024-06-09 19:06:25.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-09 19:06:25.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-09 19:06:25.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-09 19:06:25.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.848][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.852][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-09 19:06:25.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.859][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.862][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.878][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-09 19:06:25.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-09 19:06:25.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-09 19:06:25.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-09 19:06:25.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-09 19:06:25.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-09 19:06:25.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.912][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.918][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.921][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-09 19:06:25.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-09 19:06:25.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-09 19:06:25.927][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-06-09 19:06:25.928][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-09 19:06:25.929][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-09 19:06:26.008][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-09 19:06:26.014][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-09 19:06:26.058][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-09 19:06:26.059][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-09 19:06:26.060][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-09 19:06:26.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-09 19:06:26.062][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-09 19:06:26.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-09 19:06:26.063][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-09 19:06:26.064][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".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]

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

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

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

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.3250.8993.310
LipidmapsStructureEntry0.3630.0180.392