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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 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
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: 2024-06-12 14:00 -0400 (Wed, 12 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  

CHECK results for biodbLipidmaps on palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-13 01:01:59 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 01:09:37 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 458.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'biodbLipidmaps' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
LipidmapsStructureConn 3.87   3.89  207.02
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log'
for details.

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 [2024-06-13 01:07:28.492][biodb::testContext]
biodb.INFO [2024-06-13 01:07:28.496][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-13 01:07:28.497][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-13 01:07:28.499][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-13 01:07:28.500][biodb::testContext]
biodb.INFO [2024-06-13 01:07:28.508][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-13 01:07:28.511][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-13 01:07:28.520][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:07:28.522][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-13 01:07:28.523][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-13 01:07:28.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.529][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-13 01:07:28.562][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-13 01:07:28.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.567][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-13 01:07:28.568][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-13 01:07:28.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.573][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-13 01:07:28.574][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-13 01:07:28.575][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-13 01:07:28.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.580][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-13 01:07:28.581][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-13 01:07:28.582][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-13 01:07:28.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.587][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-13 01:07:28.589][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-13 01:07:28.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.594][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-13 01:07:28.595][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-13 01:07:28.597][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-13 01:07:28.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.601][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-13 01:07:28.602][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-13 01:07:28.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.606][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[2024-06-13 01:07:28.607][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-13 01:07:28.608][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-13 01:07:28.609][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-13 01:07:28.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.614][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-13 01:07:28.615][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-13 01:07:28.616][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-13 01:07:28.617][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-13 01:07:28.619][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-13 01:07:28.620][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-13 01:07:28.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.624][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-13 01:07:28.626][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-13 01:07:28.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.630][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-13 01:07:28.631][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-13 01:07:28.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.636][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-13 01:07:28.637][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-13 01:07:28.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.642][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-13 01:07:28.644][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-13 01:07:28.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.647][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[2024-06-13 01:07:28.648][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-13 01:07:28.649][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-13 01:07:28.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.654][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-13 01:07:28.655][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-13 01:07:28.659][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-13 01:07:28.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.663][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-13 01:07:28.664][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-13 01:07:28.665][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-13 01:07:28.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.672][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-13 01:07:28.699][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.714][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-13 01:07:28.716][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.717][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:07:28.718][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.720][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.721][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.722][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.724][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:07:28.725][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:07:28.726][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.727][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-13 01:07:28.728][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:07:28.729][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.731][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.732][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:07:28.732][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:07:28.732][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-13 01:07:28.732][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-13 01:07:28.732][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-13 01:07:28.733][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:07:28.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.737][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:07:28.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.746][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.747][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.748][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:07:28.749][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:07:28.750][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.752][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.753][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-13 01:07:28.755][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.756][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-13 01:07:28.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.758][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:07:28.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.761][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.763][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.764][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-13 01:07:28.766][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:07:28.767][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.768][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-13 01:07:28.769][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:07:28.770][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.772][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.773][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:07:28.773][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:07:28.773][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-13 01:07:28.773][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-13 01:07:28.773][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-13 01:07:28.774][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:07:28.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.777][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:07:28.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.780][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.781][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.782][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.783][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:07:28.785][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:07:28.786][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.787][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.788][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-13 01:07:28.790][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.792][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-13 01:07:28.793][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.794][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:07:28.795][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.796][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.800][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:07:28.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:07:28.802][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.805][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-13 01:07:28.806][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:07:28.807][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.810][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:07:28.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:07:28.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.819][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.820][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.821][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:07:28.822][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:07:28.823][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.824][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.826][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-13 01:07:28.828][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.829][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-13 01:07:28.830][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.832][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:07:28.833][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.834][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.835][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.837][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.838][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-13 01:07:28.839][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:07:28.840][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.841][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-13 01:07:28.843][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:07:28.844][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.845][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:28.846][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.847][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:07:28.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.851][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:07:28.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:28.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:28.854][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:07:28.855][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.857][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:07:28.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:07:28.859][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:28.860][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:28.863][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:07:28.864][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.879][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[2024-06-13 01:07:28.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.884][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[2024-06-13 01:07:28.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.895][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[2024-06-13 01:07:28.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.918][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[2024-06-13 01:07:28.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.924][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[2024-06-13 01:07:28.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.929][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[2024-06-13 01:07:28.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:28.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:28.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:28.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:28.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:28.969][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-13 01:07:28.973][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-13 01:07:28.975][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-13 01:07:28.976][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-13 01:07:28.978][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-13 01:07:28.980][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-13 01:07:28.981][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-13 01:07:28.983][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-13 01:07:28.984][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-13 01:07:28.986][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-13 01:07:28.988][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-13 01:07:28.989][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-13 01:07:28.991][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-13 01:07:28.992][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-13 01:07:28.994][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-13 01:07:28.995][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-13 01:07:28.997][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-13 01:07:28.999][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-13 01:07:29.000][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-13 01:07:29.002][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-13 01:07:29.003][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-13 01:07:29.005][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-13 01:07:29.006][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-13 01:07:29.008][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-13 01:07:29.010][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-13 01:07:29.011][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-13 01:07:29.013][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-13 01:07:29.014][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-13 01:07:29.016][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-13 01:07:29.020][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-13 01:07:29.021][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-13 01:07:29.023][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-13 01:07:29.024][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-13 01:07:29.026][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-13 01:07:29.027][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-13 01:07:29.029][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-13 01:07:29.030][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-13 01:07:29.032][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-13 01:07:29.034][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-13 01:07:29.035][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-13 01:07:29.037][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-13 01:07:29.038][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-13 01:07:29.040][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-13 01:07:29.042][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-13 01:07:29.043][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-13 01:07:29.045][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-13 01:07:29.046][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-13 01:07:29.048][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-13 01:07:29.050][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-13 01:07:29.051][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-13 01:07:29.053][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-13 01:07:29.054][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-13 01:07:29.056][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-13 01:07:29.057][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-13 01:07:29.061][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-13 01:07:29.062][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-13 01:07:29.064][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-13 01:07:29.066][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-13 01:07:29.068][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-13 01:07:29.069][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-13 01:07:29.071][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-13 01:07:29.073][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-13 01:07:29.074][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-13 01:07:29.076][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-13 01:07:29.077][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-13 01:07:29.079][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-13 01:07:29.081][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-13 01:07:29.083][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-13 01:07:29.084][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-13 01:07:29.086][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-13 01:07:29.087][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-13 01:07:29.089][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-13 01:07:29.090][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-13 01:07:29.092][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-13 01:07:29.093][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-13 01:07:29.095][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-13 01:07:29.097][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-13 01:07:29.098][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-13 01:07:29.100][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-13 01:07:29.102][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-13 01:07:29.103][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-13 01:07:29.105][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-13 01:07:29.106][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-13 01:07:29.142][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-13 01:07:29.145][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-13 01:07:29.148][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:07:29.149][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.151][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:07:29.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:29.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:29.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:29.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:29.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:29.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:29.902][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-13 01:07:29.912][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:07:29.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:29.916][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-13 01:07:29.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:29.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:07:29.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:29.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:07:29.922][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:29.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:07:29.925][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:07:29.926][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:07:29.927][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:29.929][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-13 01:07:29.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-13 01:07:29.931][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-13 01:07:29.933][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-13 01:07:29.934][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:07:29.934][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:07:29.935][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:07:29.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:29.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:29.939][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:07:29.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:07:29.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:07:29.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:07:29.944][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-13 01:07:29.944][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-13 01:07:29.945][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:07:29.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:07:29.947][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-13 01:07:29.949][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:07:29.954][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-13 01:07:29.956][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-13 01:07:29.980][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:07:29.981][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-13 01:07:29.985][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:07:29.990][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-13 01:07:29.994][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-13 01:07:29.995][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-13 01:07:29.997][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-13 01:07:29.998][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-13 01:07:30.560][biodb::testThat]
biodb.INFO [2024-06-13 01:07:30.562][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-13 01:07:30.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:30.565][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:30.686][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-13 01:07:30.689][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-13 01:07:30.692][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-13 01:07:30.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:30.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:30.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:30.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:30.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:30.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:30.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:07:30.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:30.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:30.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:30.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:30.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-13 01:07:30.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-13 01:07:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.801][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:30.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:30.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.810][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:30.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:30.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:30.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:30.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.866][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:30.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:30.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:30.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:30.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:30.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:30.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.897][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:30.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:30.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:30.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:30.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.914][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:30.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:30.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:30.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:30.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:30.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:30.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.938][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:30.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:30.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.946][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-13 01:07:30.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:30.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:30.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:30.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:30.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:30.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.026][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:31.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.153][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.158][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.171][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:31.208][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-13 01:07:31.217][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-13 01:07:31.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-13 01:07:31.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.224][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-13 01:07:31.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-13 01:07:31.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-13 01:07:31.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-13 01:07:31.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.239][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-13 01:07:31.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-13 01:07:31.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.338][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.344][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:31.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.396][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.399][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.402][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.438][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.440][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.442][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.471][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.483][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.485][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.515][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.536][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.538][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.540][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.573][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.575][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.577][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.594][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.600][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.605][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.611][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.612][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.615][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.616][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.632][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.634][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.637][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.644][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.646][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.648][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.656][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.658][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.661][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.671][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.673][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.681][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.691][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.692][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.696][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.706][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.708][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.710][ef$get] fields variable is a list.
biodb.INFO [2024-06-13 01:07:31.731][biodb::testThat]
biodb.INFO [2024-06-13 01:07:31.733][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-13 01:07:31.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:31.737][biodb::testThat]
biodb.DEBUG[2024-06-13 01:07:31.760][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-13 01:07:31.771][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-13 01:07:31.782][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-13 01:07:31.785][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-13 01:07:31.790][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-13 01:07:31.793][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-13 01:07:31.829][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-13 01:07:31.832][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-13 01:07:31.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:31.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:31.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:31.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:31.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:31.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:31.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:07:31.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:31.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-13 01:07:31.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-13 01:07:31.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-13 01:07:31.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-13 01:07:31.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.893][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:31.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:31.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.898][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:31.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:31.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.905][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.913][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:31.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.922][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:31.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.939][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:31.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.944][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:31.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:31.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:31.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:31.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.975][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:31.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.981][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-13 01:07:31.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.991][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:31.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:31.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:31.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:31.997][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:31.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.033][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:32.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:32.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.039][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:32.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:32.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:32.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:32.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.051][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:32.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:32.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:32.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:32.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:32.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:32.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:32.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:32.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:32.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:32.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:32.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:32.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:32.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:32.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:32.110][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-13 01:07:32.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-13 01:07:32.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-13 01:07:32.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-13 01:07:32.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-13 01:07:32.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-13 01:07:32.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-13 01:07:32.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-13 01:07:32.156][biodb::testThat]
biodb.INFO [2024-06-13 01:07:32.158][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-13 01:07:32.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:32.162][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:32.175][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.178][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.182][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:32.185][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-13 01:07:32.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:32.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:32.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:32.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:32.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:32.264][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-13 01:07:32.270][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[2024-06-13 01:07:32.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:07:32.302][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:07:32.305][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-13 01:07:33.313][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2024-06-13 01:07:33.315][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:07:33.318][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:07:33.321][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-13 01:07:34.044][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:07:34.047][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-13 01:07:34.064][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-13 01:07:34.068][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-13 01:07:34.095][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:34.097][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:34.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.099][ef$get] fields variable is a list.
biodb.INFO [2024-06-13 01:07:34.107][biodb::testThat]
biodb.INFO [2024-06-13 01:07:34.108][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-13 01:07:34.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:34.116][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:34.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:34.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:34.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:34.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:34.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:34.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:34.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:34.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-13 01:07:34.277][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-13 01:07:34.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-13 01:07:34.294][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-13 01:07:34.297][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-13 01:07:34.327][biodb::testThat]
biodb.INFO [2024-06-13 01:07:34.329][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-13 01:07:34.330][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:34.331][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:34.355][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.360][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.365][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-13 01:07:34.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-13 01:07:34.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.370][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-13 01:07:34.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-13 01:07:34.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.422][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-13 01:07:34.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.427][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-13 01:07:34.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-13 01:07:34.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:34.432][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-13 01:07:34.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-13 01:07:34.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:34.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-13 01:07:34.446][biodb::testThat]
biodb.INFO [2024-06-13 01:07:34.447][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-13 01:07:34.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:34.450][biodb::testThat]
biodb.INFO [2024-06-13 01:07:34.462][biodb::testThat]
biodb.INFO [2024-06-13 01:07:34.464][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-13 01:07:34.465][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:34.466][biodb::testThat]
biodb.INFO [2024-06-13 01:07:34.478][biodb::testThat]
biodb.INFO [2024-06-13 01:07:34.479][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-13 01:07:34.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:34.482][biodb::testThat]
biodb.DEBUG[2024-06-13 01:07:34.487][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-13 01:07:34.775][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-13 01:07:36.069][biodb::testThat]
biodb.INFO [2024-06-13 01:07:36.072][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-13 01:07:36.074][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:36.075][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:36.090][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:36.092][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:36.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.098][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.100][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.103][ef$get] fields variable is a list.
biodb.INFO [2024-06-13 01:07:36.107][biodb::testThat]
biodb.INFO [2024-06-13 01:07:36.109][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-13 01:07:36.111][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:36.112][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:36.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:36.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:36.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:36.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:36.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:36.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:36.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:36.237][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-13 01:07:36.241][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-13 01:07:36.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-13 01:07:36.245][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-13 01:07:36.248][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-13 01:07:36.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-13 01:07:36.341][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-13 01:07:36.343][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-13 01:07:36.345][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-13 01:07:36.348][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-13 01:07:36.376][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-13 01:07:36.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-13 01:07:36.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-13 01:07:36.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-13 01:07:36.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:36.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:36.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:36.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:36.460][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-13 01:07:36.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:07:36.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:07:36.496][private$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[2024-06-13 01:07:36.787][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-06-13 01:07:36.788][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:07:36.791][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:07:36.794][getBaseUrlRequestResult] Using base::url() 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[2024-06-13 01:07:42.546][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:07:42.550][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-13 01:07:42.725][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-13 01:07:44.806][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[2024-06-13 01:07:44.811][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:07:44.812][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:07:44.814][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-13 01:07:45.170][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-06-13 01:07:45.171][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:07:45.174][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:07:45.176][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-13 01:07:45.790][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:07:45.793][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-13 01:07:45.802][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-13 01:07:45.845][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-13 01:07:45.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:07:45.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:07:45.857][private$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[2024-06-13 01:07:46.160][doesRCurlRequestUrlExist] According to RCurl, URL 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 does not exist.
biodb.TRACE[2024-06-13 01:07:46.162][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:07:46.164][getUrlRequestResult] URL "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" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:07:46.166][getBaseUrlRequestResult] Using base::url() 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[2024-06-13 01:07:46.793][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:07:46.798][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-13 01:07:46.806][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-13 01:07:46.850][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-13 01:07:46.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-13 01:07:46.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:46.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-13 01:07:46.879][biodb::testThat]
biodb.INFO [2024-06-13 01:07:46.882][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-13 01:07:46.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:46.887][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:46.893][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-13 01:07:46.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-13 01:07:46.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:46.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:46.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-13 01:07:46.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-13 01:07:46.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:46.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:46.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:46.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:46.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:46.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:46.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:46.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:46.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:46.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:46.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:46.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:46.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:46.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:46.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:46.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:46.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:46.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:46.977][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[2024-06-13 01:07:46.984][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:07:46.986][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:07:46.991][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-13 01:07:47.327][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2024-06-13 01:07:47.329][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:07:47.333][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:07:47.336][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-13 01:07:53.085][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:07:53.088][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-13 01:07:53.188][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-13 01:07:54.644][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-13 01:07:54.684][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-13 01:07:54.686][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-13 01:07:54.688][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-06-13 01:07:54.700][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-13 01:07:54.702][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-13 01:07:54.703][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-13 01:07:54.705][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-13 01:07:54.706][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-13 01:07:54.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:54.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:54.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:54.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:54.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:54.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:54.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:54.724][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-13 01:07:54.728][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:07:54.730][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:07:54.732][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-13 01:07:55.046][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:07:55.047][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:07:55.048][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:07:55.050][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-13 01:07:56.584][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:07:56.588][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-13 01:07:56.594][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-13 01:07:56.598][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-13 01:07:56.601][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-13 01:07:56.602][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-13 01:07:56.604][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-13 01:07:56.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:56.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:56.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:56.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:56.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:56.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:56.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:07:56.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-13 01:07:56.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-13 01:07:56.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-13 01:07:56.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-13 01:07:56.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.647][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:56.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:56.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:56.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:56.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.658][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.670][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.681][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:56.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:56.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.688][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:56.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:56.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.694][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:56.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:56.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.700][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:56.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:56.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.718][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:56.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.724][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-13 01:07:56.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.741][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:56.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.747][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.765][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:56.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:56.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:56.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:56.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:56.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:56.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:56.803][FUN] Functions in observer BiodbConfig: [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[2024-06-13 01:07:56.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-13 01:07:56.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-13 01:07:56.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.832][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:56.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-13 01:07:56.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.838][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:56.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-13 01:07:56.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.844][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.851][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-13 01:07:56.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-13 01:07:56.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.869][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:56.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:56.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.875][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-13 01:07:56.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:56.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.881][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:56.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:56.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-13 01:07:56.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-13 01:07:56.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.904][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:56.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.910][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-13 01:07:56.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:07:56.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.944][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-13 01:07:56.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:07:56.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.949][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.954][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.964][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:56.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:56.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:56.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:56.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:56.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:57.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:57.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:57.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:57.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:07:57.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:07:57.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:57.014][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-13 01:07:57.023][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-13 01:07:57.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:57.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:57.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:57.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:57.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:57.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:57.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:07:57.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.045][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.050][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.051][private$selectFields]
biodb.TRACE[2024-06-13 01:07:57.053][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:07:57.054][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:07:57.055][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.056][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.058][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.060][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.061][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.063][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.065][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.067][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.068][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.069][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.070][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.073][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.074][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:07:57.075][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.085][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.098][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-13 01:07:57.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:57.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:57.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:57.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:57.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:57.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:57.113][FUN] Functions in observer BiodbConfig: [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[2024-06-13 01:07:57.114][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.124][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.126][private$selectFields]
biodb.TRACE[2024-06-13 01:07:57.127][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:07:57.128][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:07:57.129][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.130][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.132][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.134][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.135][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.137][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.139][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.140][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.142][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.143][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.144][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.148][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:07:57.149][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.154][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.159][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.165][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-13 01:07:57.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:57.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:57.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:57.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:57.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:57.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:57.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:07:57.181][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.186][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.191][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.192][private$selectFields]
biodb.TRACE[2024-06-13 01:07:57.193][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:07:57.194][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:07:57.196][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.197][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.198][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.202][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.203][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.206][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.207][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.208][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:07:57.210][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.211][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.214][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.215][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:07:57.216][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.221][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.226][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:07:57.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.232][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-13 01:07:57.233][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-13 01:07:57.234][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-13 01:07:57.246][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-13 01:07:57.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-13 01:07:57.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-13 01:07:57.258][biodb::testThat]
biodb.INFO [2024-06-13 01:07:57.259][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-13 01:07:57.260][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:07:57.262][biodb::testThat]
biodb.TRACE[2024-06-13 01:07:57.266][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-13 01:07:57.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-13 01:07:57.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-13 01:07:57.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-13 01:07:57.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:07:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:07:57.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:07:57.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:07:57.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:07:57.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:07:57.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:07:57.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:07:57.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:07:57.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:07:57.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:07:57.375][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-06-13 01:07:57.381][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:07:57.383][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:07:57.386][private$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[2024-06-13 01:07:57.699][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375 does not exist.
biodb.TRACE[2024-06-13 01:07:57.701][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:07:57.703][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:07:57.706][getBaseUrlRequestResult] Using base::url() 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[2024-06-13 01:08:03.227][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:03.230][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-13 01:08:03.322][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-13 01:08:05.012][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-13 01:08:05.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:05.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:05.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:05.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:05.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:05.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:05.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:08:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.069][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.094][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.095][private$selectFields]
biodb.TRACE[2024-06-13 01:08:05.096][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:08:05.097][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:08:05.099][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.100][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.101][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.104][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.105][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.106][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.109][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.110][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.121][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.122][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.124][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.126][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.127][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:08:05.128][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.139][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.145][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-13 01:08:05.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:05.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:05.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:05.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:05.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:05.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:05.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:08:05.163][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.169][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.174][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.175][private$selectFields]
biodb.TRACE[2024-06-13 01:08:05.176][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:08:05.177][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:08:05.178][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.180][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.181][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.184][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.185][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.187][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.190][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.192][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.193][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.194][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.197][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.198][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:08:05.199][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.205][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.210][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.216][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-13 01:08:05.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:05.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:05.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:05.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:05.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:05.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:05.231][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.TRACE[2024-06-13 01:08:05.232][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.237][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.242][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.244][private$selectFields]
biodb.TRACE[2024-06-13 01:08:05.245][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:08:05.246][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:08:05.247][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.249][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.250][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.252][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.254][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.255][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.257][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.259][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.260][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:05.261][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.263][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.265][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.266][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:08:05.268][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.274][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:05.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.287][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-13 01:08:05.288][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-13 01:08:05.290][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-13 01:08:05.302][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-13 01:08:05.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-13 01:08:05.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-13 01:08:05.316][biodb::testThat]
biodb.INFO [2024-06-13 01:08:05.318][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-13 01:08:05.319][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:05.321][biodb::testThat]
biodb.TRACE[2024-06-13 01:08:05.325][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-13 01:08:05.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-13 01:08:05.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-13 01:08:05.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-13 01:08:05.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:05.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:05.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:05.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:08:05.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:05.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:05.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:05.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:05.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:05.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:05.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:05.412][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[2024-06-13 01:08:05.416][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-13 01:08:05.417][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-13 01:08:05.419][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-13 01:08:05.555][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-13 01:08:07.267][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-13 01:08:07.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:07.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:07.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:07.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:07.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:07.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:07.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:08:07.284][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.289][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.295][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.297][private$selectFields]
biodb.TRACE[2024-06-13 01:08:07.298][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:08:07.299][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:08:07.300][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.301][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.303][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.305][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.306][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.307][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.310][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.311][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.312][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.313][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.316][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.318][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.320][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:08:07.321][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.326][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.331][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.336][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-13 01:08:07.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:07.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:07.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:07.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:07.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:07.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:07.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:08:07.353][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.358][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.363][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.364][private$selectFields]
biodb.TRACE[2024-06-13 01:08:07.365][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:08:07.366][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:08:07.368][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.369][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.370][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.373][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.374][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.375][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.379][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.380][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.381][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.383][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.385][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.386][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:08:07.387][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.393][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.398][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.404][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-13 01:08:07.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:07.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:07.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:07.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:07.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:07.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:07.418][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.TRACE[2024-06-13 01:08:07.420][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.425][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.429][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.431][private$selectFields]
biodb.TRACE[2024-06-13 01:08:07.432][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-13 01:08:07.433][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-13 01:08:07.434][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.435][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.437][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.441][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.442][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.444][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.445][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.447][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-13 01:08:07.448][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.449][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.451][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.453][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-13 01:08:07.455][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.460][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.465][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:07.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:07.470][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-13 01:08:07.472][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-13 01:08:07.473][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-13 01:08:07.500][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-13 01:08:07.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-13 01:08:07.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:07.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-13 01:08:07.511][biodb::testThat]
biodb.INFO [2024-06-13 01:08:07.512][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-13 01:08:07.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:07.514][biodb::testThat]
biodb.DEBUG[2024-06-13 01:08:07.516][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-13 01:08:07.518][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-13 01:08:07.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.INFO [2024-06-13 01:08:07.521][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-06-13 01:08:07.523][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-13 01:08:07.525][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-13 01:08:07.526][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-13 01:08:07.528][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-13 01:08:07.529][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-13 01:08:07.530][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-13 01:08:07.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:07.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:07.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:07.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:07.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:07.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:07.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:07.566][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-13 01:08:07.569][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:07.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:08:07.572][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:07.877][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:07.879][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:07.880][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:07.881][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:08.472][private$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[2024-06-13 01:08:08.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:08.474][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:08.476][rule$waitAsNeeded] Wait 0.096231 second(s).
biodb.TRACE[2024-06-13 01:08:08.578][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:08.869][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:08.870][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:08.872][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[2024-06-13 01:08:08.873][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:09.473][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:09.474][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:09.476][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:09.477][rule$waitAsNeeded] Wait 0.100468 second(s).
biodb.TRACE[2024-06-13 01:08:09.581][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:09.874][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:09.876][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:09.877][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:09.878][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:10.475][private$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[2024-06-13 01:08:10.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:10.479][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:10.481][rule$waitAsNeeded] Wait 0.099267 second(s).
biodb.TRACE[2024-06-13 01:08:10.583][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:10.871][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:10.873][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:10.874][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[2024-06-13 01:08:10.875][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:11.464][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:11.466][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:11.468][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:11.470][rule$waitAsNeeded] Wait 0.112927 second(s).
biodb.TRACE[2024-06-13 01:08:11.585][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:11.874][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:11.876][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:11.877][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:11.879][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:12.562][private$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[2024-06-13 01:08:12.563][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:12.564][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:12.566][rule$waitAsNeeded] Wait 0.0187812 second(s).
biodb.TRACE[2024-06-13 01:08:12.587][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:12.885][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:12.888][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:12.890][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[2024-06-13 01:08:12.892][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:13.481][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:13.483][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:13.485][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:13.488][rule$waitAsNeeded] Wait 0.0992589 second(s).
biodb.TRACE[2024-06-13 01:08:13.605][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:13.896][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:13.898][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:13.900][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:13.901][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:14.509][private$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[2024-06-13 01:08:14.512][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:14.514][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:14.518][rule$waitAsNeeded] Wait 0.0866749 second(s).
biodb.TRACE[2024-06-13 01:08:14.622][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:14.943][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:14.946][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:14.947][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[2024-06-13 01:08:14.948][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:15.532][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:15.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:15.537][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:15.539][rule$waitAsNeeded] Wait 0.0828049 second(s).
biodb.TRACE[2024-06-13 01:08:15.640][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:15.940][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:15.942][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:15.943][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:15.944][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:16.534][private$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[2024-06-13 01:08:16.536][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:16.538][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:16.540][rule$waitAsNeeded] Wait 0.0990222 second(s).
biodb.TRACE[2024-06-13 01:08:16.657][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-13 01:08:16.953][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:16.955][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:16.957][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[2024-06-13 01:08:16.958][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-13 01:08:17.551][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.INFO [2024-06-13 01:08:17.556][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-06-13 01:08:17.559][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-13 01:08:17.563][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-13 01:08:17.566][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-13 01:08:17.569][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-13 01:08:17.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:17.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:17.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:17.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:17.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:17.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:17.592][FUN] Functions in observer BiodbConfig: [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[2024-06-13 01:08:17.596][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:17.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:17.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:17.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:17.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:17.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:17.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:17.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:17.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:17.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:17.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:17.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:17.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:17.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:17.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:17.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:17.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:17.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:17.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:17.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:17.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:17.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:08:17.659][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-13 01:08:17.661][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-13 01:08:17.682][biodb::testThat]
biodb.INFO [2024-06-13 01:08:17.684][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-13 01:08:17.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:17.688][biodb::testThat]
biodb.DEBUG[2024-06-13 01:08:17.707][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-13 01:08:17.708][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-13 01:08:17.710][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-13 01:08:17.713][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-13 01:08:17.715][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-13 01:08:17.716][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-13 01:08:17.718][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-13 01:08:17.719][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-13 01:08:17.721][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-13 01:08:17.722][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-13 01:08:17.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:17.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:17.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:17.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:17.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:17.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:17.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:17.747][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-13 01:08:17.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:17.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:08:17.753][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:18.054][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:18.057][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:18.059][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[2024-06-13 01:08:18.061][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:18.662][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:18.665][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:18.667][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:18.669][rule$waitAsNeeded] Wait 0.0841479 second(s).
biodb.TRACE[2024-06-13 01:08:18.771][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:19.061][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:19.063][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:19.065][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:19.067][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:19.665][private$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[2024-06-13 01:08:19.667][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:19.668][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:19.670][rule$waitAsNeeded] Wait 0.0998561 second(s).
biodb.TRACE[2024-06-13 01:08:19.773][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:20.083][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:20.084][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:20.086][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[2024-06-13 01:08:20.088][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:20.686][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:20.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:20.690][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:20.692][rule$waitAsNeeded] Wait 0.0807402 second(s).
biodb.TRACE[2024-06-13 01:08:20.779][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:21.074][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:21.075][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:21.077][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:21.078][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:21.668][private$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[2024-06-13 01:08:21.671][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:21.673][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:21.675][rule$waitAsNeeded] Wait 0.10373 second(s).
biodb.TRACE[2024-06-13 01:08:21.784][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:22.100][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:22.102][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:22.104][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[2024-06-13 01:08:22.107][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:22.710][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:22.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:22.714][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:22.716][rule$waitAsNeeded] Wait 0.067163 second(s).
biodb.TRACE[2024-06-13 01:08:22.786][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:23.092][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:23.094][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:23.095][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:23.097][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:23.712][private$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[2024-06-13 01:08:23.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:23.717][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:23.719][rule$waitAsNeeded] Wait 0.0662942 second(s).
biodb.TRACE[2024-06-13 01:08:23.788][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:24.091][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:24.093][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:24.094][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[2024-06-13 01:08:24.095][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:24.693][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:24.694][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:24.696][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:24.697][rule$waitAsNeeded] Wait 0.0904701 second(s).
biodb.TRACE[2024-06-13 01:08:24.791][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:25.099][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:25.100][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:25.102][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:25.103][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:25.701][private$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[2024-06-13 01:08:25.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:25.706][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:25.708][rule$waitAsNeeded] Wait 0.0825908 second(s).
biodb.TRACE[2024-06-13 01:08:25.809][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:26.121][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:26.123][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:26.125][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[2024-06-13 01:08:26.127][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:26.784][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:26.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:26.788][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:26.790][rule$waitAsNeeded] Wait 0.0189772 second(s).
biodb.TRACE[2024-06-13 01:08:26.812][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-13 01:08:27.107][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:27.109][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:27.110][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:27.111][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-13 01:08:27.706][private$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[2024-06-13 01:08:27.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:27.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:27.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:27.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:27.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:27.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:27.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:27.733][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-13 01:08:27.738][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:27.740][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:27.742][rule$waitAsNeeded] Wait 0.069519 second(s).
biodb.TRACE[2024-06-13 01:08:27.830][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:28.131][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:28.132][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:28.134][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:28.135][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:28.726][private$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[2024-06-13 01:08:28.728][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:28.730][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:28.732][rule$waitAsNeeded] Wait 0.0969219 second(s).
biodb.TRACE[2024-06-13 01:08:28.832][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:29.129][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:29.130][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:29.132][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[2024-06-13 01:08:29.133][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:29.758][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:29.760][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:29.763][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:29.765][rule$waitAsNeeded] Wait 0.0668468 second(s).
biodb.TRACE[2024-06-13 01:08:29.850][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:30.178][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:30.180][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:30.182][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:30.183][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:30.778][private$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[2024-06-13 01:08:30.780][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:30.782][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:30.785][rule$waitAsNeeded] Wait 0.0651641 second(s).
biodb.TRACE[2024-06-13 01:08:30.855][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:31.156][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:31.157][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:31.159][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[2024-06-13 01:08:31.160][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:31.752][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:31.754][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:31.756][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:31.757][rule$waitAsNeeded] Wait 0.096441 second(s).
biodb.TRACE[2024-06-13 01:08:31.860][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:32.158][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:32.160][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:32.161][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:32.163][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:32.774][private$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[2024-06-13 01:08:32.776][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:32.778][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:32.780][rule$waitAsNeeded] Wait 0.0796862 second(s).
biodb.TRACE[2024-06-13 01:08:32.866][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:33.184][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:33.185][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:33.187][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[2024-06-13 01:08:33.188][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:33.809][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:33.811][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:33.812][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:33.815][rule$waitAsNeeded] Wait 0.0513189 second(s).
biodb.TRACE[2024-06-13 01:08:33.870][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:34.197][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:34.200][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:34.202][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:34.204][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:34.812][private$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[2024-06-13 01:08:34.814][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:34.816][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:34.819][rule$waitAsNeeded] Wait 0.0507989 second(s).
biodb.TRACE[2024-06-13 01:08:34.889][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:35.185][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:35.187][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:35.189][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[2024-06-13 01:08:35.191][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:35.783][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:08:35.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:35.787][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:35.808][rule$waitAsNeeded] Wait 0.0990319 second(s).
biodb.TRACE[2024-06-13 01:08:35.922][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:36.222][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:36.224][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:36.225][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:36.227][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:37.036][private$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[2024-06-13 01:08:37.038][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:37.040][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:08:37.043][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-13 01:08:37.340][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:08:37.341][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:37.343][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:37.344][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-13 01:08:38.148][private$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[2024-06-13 01:08:38.152][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-13 01:08:38.156][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-13 01:08:38.158][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-13 01:08:38.160][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-13 01:08:38.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:38.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:38.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:38.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:38.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:38.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:38.175][FUN] Functions in observer BiodbConfig: [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[2024-06-13 01:08:38.177][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.183][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:08:38.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:08:38.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:38.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:38.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:38.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:38.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:38.206][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.TRACE[2024-06-13 01:08:38.208][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.214][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:08:38.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:38.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:08:38.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:08:38.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:38.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:08:38.280][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-13 01:08:38.281][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-13 01:08:38.282][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-13 01:08:38.676][biodb::testThat]
biodb.INFO [2024-06-13 01:08:38.678][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-13 01:08:38.681][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:38.683][biodb::testThat]
biodb.INFO [2024-06-13 01:08:38.746][biodb::testThat]
biodb.INFO [2024-06-13 01:08:38.749][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-13 01:08:38.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:38.753][biodb::testThat]
biodb.INFO [2024-06-13 01:08:38.771][biodb::testThat]
biodb.INFO [2024-06-13 01:08:38.773][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-13 01:08:38.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:38.775][biodb::testThat]
biodb.DEBUG[2024-06-13 01:08:38.781][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[2024-06-13 01:08:38.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:38.790][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:08:38.792][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-13 01:08:39.091][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV does not exist.
biodb.TRACE[2024-06-13 01:08:39.092][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:39.094][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:39.096][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-13 01:08:45.826][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:45.829][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-13 01:08:46.176][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-13 01:08:47.963][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-13 01:08:47.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-13 01:08:47.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:47.967][ef$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:08:47.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:47.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-13 01:08:47.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:08:47.972][ef$get] fields variable is a list.
biodb.INFO [2024-06-13 01:08:47.974][biodb::testThat]
biodb.INFO [2024-06-13 01:08:47.975][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-13 01:08:47.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:47.978][biodb::testThat]
biodb.ERROR[2024-06-13 01:08:48.002][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-13 01:08:48.025][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-13 01:08:48.043][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-13 01:08:48.045][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-13 01:08:48.047][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-13 01:08:48.048][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-13 01:08:48.049][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.051][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.054][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-13 01:08:48.070][biodb::testContext]
biodb.INFO [2024-06-13 01:08:48.071][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-13 01:08:48.073][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-13 01:08:48.074][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-13 01:08:48.076][biodb::testContext]
biodb.INFO [2024-06-13 01:08:48.080][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-13 01:08:48.084][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-13 01:08:48.094][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:08:48.096][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-13 01:08:48.098][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-13 01:08:48.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.106][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-13 01:08:48.108][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-13 01:08:48.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.115][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-13 01:08:48.117][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-13 01:08:48.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.122][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[2024-06-13 01:08:48.124][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-13 01:08:48.125][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-13 01:08:48.127][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-13 01:08:48.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.133][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-13 01:08:48.134][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-13 01:08:48.136][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-13 01:08:48.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.140][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-13 01:08:48.142][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-13 01:08:48.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.147][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-13 01:08:48.148][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-13 01:08:48.149][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-13 01:08:48.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.153][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[2024-06-13 01:08:48.154][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-13 01:08:48.156][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-13 01:08:48.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.161][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-13 01:08:48.162][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-13 01:08:48.164][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-13 01:08:48.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.169][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-13 01:08:48.170][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-13 01:08:48.171][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-13 01:08:48.172][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-13 01:08:48.174][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-13 01:08:48.175][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-13 01:08:48.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.180][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-13 01:08:48.181][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-13 01:08:48.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.189][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-13 01:08:48.191][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-13 01:08:48.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.199][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-13 01:08:48.201][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-13 01:08:48.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.204][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[2024-06-13 01:08:48.205][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-13 01:08:48.207][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-13 01:08:48.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.212][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-13 01:08:48.213][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-13 01:08:48.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.218][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-13 01:08:48.219][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-13 01:08:48.223][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-13 01:08:48.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.229][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-13 01:08:48.230][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-13 01:08:48.231][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-13 01:08:48.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.237][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-13 01:08:48.239][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.241][self$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[2024-06-13 01:08:48.242][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.243][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:48.244][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.247][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.248][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.250][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:08:48.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:48.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.253][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-13 01:08:48.255][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:48.256][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.258][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.260][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:08:48.260][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:08:48.260][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-13 01:08:48.260][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-13 01:08:48.260][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-13 01:08:48.262][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:48.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.268][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:48.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.273][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.275][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.277][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:48.279][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:48.281][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.283][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.285][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-13 01:08:48.290][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.292][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-13 01:08:48.294][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:48.298][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.299][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.301][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.302][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.304][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-13 01:08:48.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:48.306][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.308][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-13 01:08:48.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:48.311][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:08:48.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:08:48.313][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-13 01:08:48.313][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-13 01:08:48.313][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-13 01:08:48.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:48.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.319][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:48.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.324][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.326][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:48.328][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:48.329][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.331][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.333][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-13 01:08:48.337][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.339][self$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[2024-06-13 01:08:48.340][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.341][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:48.343][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.344][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.345][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.348][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:08:48.349][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:48.350][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.351][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-13 01:08:48.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:48.355][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.357][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.359][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.361][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:48.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.367][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:48.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.373][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.375][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:48.378][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:48.379][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.394][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.396][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-13 01:08:48.398][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.400][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-13 01:08:48.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.402][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:48.403][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.409][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.411][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-13 01:08:48.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:48.414][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.416][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-13 01:08:48.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:48.420][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.421][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.422][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.424][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:48.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.428][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:48.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.431][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.433][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:48.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:48.436][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.437][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.439][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:08:48.440][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.489][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[2024-06-13 01:08:48.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.560][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-13 01:08:48.562][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-13 01:08:48.565][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-13 01:08:48.568][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-13 01:08:48.571][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-13 01:08:48.573][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-13 01:08:48.576][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-13 01:08:48.578][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-13 01:08:48.581][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-13 01:08:48.584][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-13 01:08:48.586][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-13 01:08:48.589][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-13 01:08:48.592][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-13 01:08:48.594][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-13 01:08:48.597][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-13 01:08:48.600][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-13 01:08:48.603][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-13 01:08:48.605][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-13 01:08:48.608][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-13 01:08:48.611][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-13 01:08:48.614][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-13 01:08:48.617][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-13 01:08:48.620][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-13 01:08:48.622][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-13 01:08:48.625][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-13 01:08:48.628][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-13 01:08:48.631][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-13 01:08:48.634][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-13 01:08:48.636][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-13 01:08:48.639][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-13 01:08:48.642][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-13 01:08:48.645][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-13 01:08:48.647][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-13 01:08:48.650][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-13 01:08:48.652][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-13 01:08:48.654][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-13 01:08:48.656][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-13 01:08:48.657][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-13 01:08:48.659][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-13 01:08:48.661][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-13 01:08:48.663][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-13 01:08:48.664][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-13 01:08:48.666][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-13 01:08:48.668][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-13 01:08:48.670][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-13 01:08:48.671][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-13 01:08:48.673][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-13 01:08:48.675][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-13 01:08:48.676][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-13 01:08:48.678][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-13 01:08:48.679][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-13 01:08:48.681][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-13 01:08:48.683][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-13 01:08:48.684][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-13 01:08:48.686][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-13 01:08:48.688][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-13 01:08:48.689][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-13 01:08:48.691][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-13 01:08:48.692][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-13 01:08:48.694][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-13 01:08:48.696][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-13 01:08:48.697][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-13 01:08:48.699][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-13 01:08:48.701][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-13 01:08:48.703][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-13 01:08:48.705][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-13 01:08:48.707][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-13 01:08:48.708][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-13 01:08:48.710][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-13 01:08:48.711][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-13 01:08:48.713][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-13 01:08:48.715][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-13 01:08:48.716][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-13 01:08:48.718][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-13 01:08:48.720][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-13 01:08:48.721][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-13 01:08:48.723][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-13 01:08:48.725][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-13 01:08:48.726][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-13 01:08:48.728][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-13 01:08:48.730][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-13 01:08:48.731][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-13 01:08:48.733][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-13 01:08:48.735][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-13 01:08:48.738][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-13 01:08:48.739][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:08:48.740][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.743][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.753][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[2024-06-13 01:08:48.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.791][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[2024-06-13 01:08:48.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.822][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[2024-06-13 01:08:48.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.830][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[2024-06-13 01:08:48.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:48.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:48.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:48.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:48.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:48.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:48.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:48.929][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-13 01:08:48.931][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:08:48.933][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.935][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.936][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.937][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:48.939][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.940][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.941][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.944][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:08:48.945][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:48.947][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.948][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-13 01:08:48.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-13 01:08:48.950][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-13 01:08:48.952][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:48.953][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:08:48.953][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:08:48.954][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:48.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.957][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:48.959][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:48.960][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:48.961][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:48.962][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-13 01:08:48.962][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-13 01:08:48.963][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:48.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:48.965][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:48.967][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:48.968][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-13 01:08:48.970][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-13 01:08:48.973][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:08:48.974][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-13 01:08:48.976][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:08:48.978][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-13 01:08:48.979][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-13 01:08:48.980][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-13 01:08:48.982][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-13 01:08:48.983][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-13 01:08:48.986][biodb::testThat]
biodb.INFO [2024-06-13 01:08:48.987][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-13 01:08:48.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:48.989][biodb::testThat]
biodb.DEBUG[2024-06-13 01:08:48.994][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-06-13 01:08:48.999][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:49.000][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:08:49.002][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-13 01:08:49.314][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride does not exist.
biodb.TRACE[2024-06-13 01:08:49.315][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:49.317][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:49.319][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-06-13 01:08:49.925][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:49.929][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-13 01:08:49.937][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-13 01:08:49.953][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[2024-06-13 01:08:49.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:49.959][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:49.960][rule$waitAsNeeded] Wait 0.0418069 second(s).
biodb.TRACE[2024-06-13 01:08:50.018][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-13 01:08:50.314][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty does not exist.
biodb.TRACE[2024-06-13 01:08:50.316][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:50.318][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:50.319][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-13 01:08:50.912][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:50.917][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-13 01:08:50.925][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-13 01:08:50.950][biodb::testThat]
biodb.INFO [2024-06-13 01:08:50.952][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-13 01:08:50.954][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:50.956][biodb::testThat]
biodb.INFO [2024-06-13 01:08:50.993][biodb::testThat]
biodb.INFO [2024-06-13 01:08:50.995][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-13 01:08:50.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:50.997][biodb::testThat]
biodb.DEBUG[2024-06-13 01:08:51.001][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[2024-06-13 01:08:51.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:51.007][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:51.008][rule$waitAsNeeded] Wait 0.00854206 second(s).
biodb.TRACE[2024-06-13 01:08:51.021][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-13 01:08:51.324][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-06-13 01:08:51.326][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:51.327][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:51.329][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-13 01:08:51.744][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:51.748][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-13 01:08:51.756][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-13 01:08:51.766][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[2024-06-13 01:08:51.772][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-13 01:08:51.775][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-13 01:08:51.777][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-13 01:08:51.788][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-13 01:08:51.799][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[2024-06-13 01:08:51.805][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:51.806][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:51.808][rule$waitAsNeeded] Wait 0.211238 second(s).
biodb.TRACE[2024-06-13 01:08:52.023][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-13 01:08:52.340][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-06-13 01:08:52.342][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:52.345][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:52.348][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-13 01:08:52.814][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:52.831][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-13 01:08:52.837][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-13 01:08:52.847][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[2024-06-13 01:08:52.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:52.853][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:08:52.854][rule$waitAsNeeded] Wait 0.167033 second(s).
biodb.TRACE[2024-06-13 01:08:53.026][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-13 01:08:53.320][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2024-06-13 01:08:53.322][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:53.323][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:53.325][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-13 01:08:54.752][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:54.757][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-13 01:08:54.776][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-13 01:08:55.016][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[2024-06-13 01:08:55.020][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:08:55.022][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:08:55.025][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-13 01:08:55.330][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6 does not exist.
biodb.TRACE[2024-06-13 01:08:55.332][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:08:55.334][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:08:55.335][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-13 01:08:56.920][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-13 01:08:56.924][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-13 01:08:56.947][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-13 01:08:57.210][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-13 01:08:57.213][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-13 01:08:57.215][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-13 01:08:57.217][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-13 01:08:57.219][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.222][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.226][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-13 01:08:57.235][biodb::testContext]
biodb.INFO [2024-06-13 01:08:57.237][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-13 01:08:57.239][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-13 01:08:57.241][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-13 01:08:57.242][biodb::testContext]
biodb.INFO [2024-06-13 01:08:57.247][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-13 01:08:57.250][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-13 01:08:57.258][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:08:57.260][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-13 01:08:57.261][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-13 01:08:57.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.266][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-13 01:08:57.267][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-13 01:08:57.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.272][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-13 01:08:57.273][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-13 01:08:57.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.278][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-13 01:08:57.279][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-13 01:08:57.280][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-13 01:08:57.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.286][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-13 01:08:57.287][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-13 01:08:57.289][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-13 01:08:57.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.293][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-13 01:08:57.295][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-13 01:08:57.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.299][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-13 01:08:57.300][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-13 01:08:57.302][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-13 01:08:57.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.306][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-13 01:08:57.308][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-13 01:08:57.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.312][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-13 01:08:57.313][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-13 01:08:57.315][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-13 01:08:57.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.319][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-13 01:08:57.320][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-13 01:08:57.322][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-13 01:08:57.324][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-13 01:08:57.326][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-13 01:08:57.329][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-13 01:08:57.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.336][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-13 01:08:57.338][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-13 01:08:57.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.345][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-13 01:08:57.347][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-13 01:08:57.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.355][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-13 01:08:57.357][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-13 01:08:57.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.362][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-13 01:08:57.363][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-13 01:08:57.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.368][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-13 01:08:57.369][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-13 01:08:57.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.374][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-13 01:08:57.375][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-13 01:08:57.380][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-13 01:08:57.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.384][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-13 01:08:57.385][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-13 01:08:57.387][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-13 01:08:57.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.390][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[2024-06-13 01:08:57.391][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-13 01:08:57.393][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.395][self$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[2024-06-13 01:08:57.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.397][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:57.398][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.402][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.406][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:08:57.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:57.410][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.412][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-13 01:08:57.414][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:57.416][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.417][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.419][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:08:57.419][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:08:57.419][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-13 01:08:57.419][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-13 01:08:57.419][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-13 01:08:57.420][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:57.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.423][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:57.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.427][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.428][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.429][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:57.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:57.432][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.433][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.435][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-13 01:08:57.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-13 01:08:57.439][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.441][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:57.442][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.444][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.445][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.447][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-13 01:08:57.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:57.450][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.451][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-13 01:08:57.452][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:57.453][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.455][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.456][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:08:57.456][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:08:57.456][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-13 01:08:57.456][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-13 01:08:57.456][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-13 01:08:57.458][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:57.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.463][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:57.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.466][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.468][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.469][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:57.470][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:57.471][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.473][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.474][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-13 01:08:57.476][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.477][self$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[2024-06-13 01:08:57.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.480][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:57.481][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.482][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.483][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.484][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.486][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:08:57.487][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:57.488][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.489][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-13 01:08:57.491][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:57.492][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.493][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.494][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.495][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:57.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:57.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.504][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:57.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:57.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.508][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.510][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-13 01:08:57.512][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.513][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-13 01:08:57.530][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:57.534][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.536][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.538][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.539][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-13 01:08:57.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:57.541][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.543][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-13 01:08:57.544][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:57.545][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.546][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.548][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.549][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:57.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.553][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:57.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.555][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.556][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.557][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.559][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:57.560][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:57.561][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.562][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:57.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:08:57.565][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.594][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[2024-06-13 01:08:57.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.617][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[2024-06-13 01:08:57.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.664][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-13 01:08:57.665][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-13 01:08:57.667][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-13 01:08:57.669][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-13 01:08:57.670][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-13 01:08:57.672][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-13 01:08:57.673][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-13 01:08:57.675][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-13 01:08:57.677][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-13 01:08:57.678][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-13 01:08:57.680][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-13 01:08:57.681][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-13 01:08:57.683][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-13 01:08:57.684][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-13 01:08:57.686][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-13 01:08:57.688][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-13 01:08:57.689][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-13 01:08:57.691][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-13 01:08:57.692][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-13 01:08:57.694][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-13 01:08:57.696][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-13 01:08:57.697][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-13 01:08:57.699][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-13 01:08:57.700][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-13 01:08:57.702][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-13 01:08:57.704][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-13 01:08:57.706][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-13 01:08:57.709][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-13 01:08:57.711][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-13 01:08:57.712][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-13 01:08:57.714][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-13 01:08:57.716][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-13 01:08:57.717][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-13 01:08:57.719][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-13 01:08:57.720][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-13 01:08:57.722][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-13 01:08:57.724][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-13 01:08:57.725][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-13 01:08:57.727][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-13 01:08:57.728][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-13 01:08:57.730][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-13 01:08:57.732][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-13 01:08:57.733][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-13 01:08:57.735][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-13 01:08:57.737][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-13 01:08:57.738][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-13 01:08:57.740][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-13 01:08:57.741][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-13 01:08:57.743][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-13 01:08:57.745][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-13 01:08:57.746][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-13 01:08:57.748][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-13 01:08:57.749][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-13 01:08:57.751][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-13 01:08:57.752][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-13 01:08:57.754][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-13 01:08:57.756][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-13 01:08:57.757][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-13 01:08:57.759][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-13 01:08:57.760][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-13 01:08:57.762][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-13 01:08:57.764][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-13 01:08:57.765][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-13 01:08:57.767][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-13 01:08:57.768][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-13 01:08:57.770][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-13 01:08:57.772][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-13 01:08:57.774][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-13 01:08:57.775][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-13 01:08:57.777][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-13 01:08:57.778][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-13 01:08:57.780][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-13 01:08:57.781][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-13 01:08:57.783][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-13 01:08:57.785][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-13 01:08:57.787][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-13 01:08:57.789][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-13 01:08:57.792][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-13 01:08:57.794][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-13 01:08:57.797][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-13 01:08:57.799][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-13 01:08:57.801][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-13 01:08:57.804][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-13 01:08:57.806][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-13 01:08:57.810][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-13 01:08:57.812][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-13 01:08:57.813][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.816][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.817][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[2024-06-13 01:08:57.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.833][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[2024-06-13 01:08:57.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.877][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[2024-06-13 01:08:57.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.885][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[2024-06-13 01:08:57.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.939][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[2024-06-13 01:08:57.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-13 01:08:57.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:08:57.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:08:57.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:08:57.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:08:57.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:08:57.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:08:57.968][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-13 01:08:57.970][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:08:57.972][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.973][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.974][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-13 01:08:57.977][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.978][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.979][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.980][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-13 01:08:57.982][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-13 01:08:57.983][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-13 01:08:57.984][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:57.985][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-13 01:08:57.986][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-13 01:08:57.988][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-13 01:08:57.989][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-13 01:08:57.990][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-13 01:08:57.990][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-13 01:08:57.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-13 01:08:57.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.995][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-13 01:08:57.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-13 01:08:57.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-13 01:08:57.998][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-13 01:08:58.000][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-13 01:08:58.000][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-13 01:08:58.001][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-13 01:08:58.002][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-13 01:08:58.003][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-13 01:08:58.004][self$setPropertyValue]
biodb.DEBUG[2024-06-13 01:08:58.006][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-13 01:08:58.008][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-13 01:08:58.011][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:08:58.012][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-13 01:08:58.014][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-13 01:08:58.016][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-13 01:08:58.017][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-13 01:08:58.019][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-13 01:08:58.020][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-13 01:08:58.022][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-13 01:08:58.024][biodb::testThat]
biodb.INFO [2024-06-13 01:08:58.025][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-13 01:08:58.026][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-13 01:08:58.027][biodb::testThat]
biodb.DEBUG[2024-06-13 01:08:58.031][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-13 01:08:58.037][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-13 01:08:58.039][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-13 01:08:58.040][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-13 01:08:58.170][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-13 01:09:00.064][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-13 01:09:00.065][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-13 01:09:00.067][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-13 01:09:00.069][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-13 01:09:00.070][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-13 01:09:00.072][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-13 01:09:00.073][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-13 01:09:00.074][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-13 01:09:00.076][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-13 01:09:00.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:09:00.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:09:00.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:09:00.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:09:00.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:09:00.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:09:00.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:09:00.095][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-06-13 01:09:00.098][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:00.099][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:09:00.100][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:00.409][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:00.411][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:00.414][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:00.416][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:00.881][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:00.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:00.884][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:00.886][rule$waitAsNeeded] Wait 0.214953 second(s).
biodb.TRACE[2024-06-13 01:09:01.107][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:01.424][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:01.426][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:01.429][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:01.431][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:02.236][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:02.238][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:02.240][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-13 01:09:02.243][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:02.565][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:02.567][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:02.568][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:02.570][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:03.176][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:03.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:03.180][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:03.182][rule$waitAsNeeded] Wait 0.060539 second(s).
biodb.TRACE[2024-06-13 01:09:03.253][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:03.569][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:03.571][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:03.574][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:03.576][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:04.193][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:04.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:04.198][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:04.200][rule$waitAsNeeded] Wait 0.0522289 second(s).
biodb.TRACE[2024-06-13 01:09:04.270][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:04.578][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:04.580][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:04.582][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:04.584][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:05.180][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:05.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:05.184][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:05.187][rule$waitAsNeeded] Wait 0.0830691 second(s).
biodb.TRACE[2024-06-13 01:09:05.272][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:05.587][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:05.588][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:05.590][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:05.592][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:06.214][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:06.216][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:06.218][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:06.220][rule$waitAsNeeded] Wait 0.0518599 second(s).
biodb.TRACE[2024-06-13 01:09:06.275][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:06.605][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:06.606][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:06.608][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:06.609][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:07.216][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:07.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:07.221][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:07.223][rule$waitAsNeeded] Wait 0.051558 second(s).
biodb.TRACE[2024-06-13 01:09:07.293][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:07.600][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:07.601][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:07.603][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:07.604][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:08.203][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:08.205][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:08.207][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:08.210][rule$waitAsNeeded] Wait 0.0828531 second(s).
biodb.TRACE[2024-06-13 01:09:08.311][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:08.606][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:08.608][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:08.610][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:08.613][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:09.208][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:09.210][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:09.213][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:09.216][rule$waitAsNeeded] Wait 0.0946078 second(s).
biodb.TRACE[2024-06-13 01:09:09.318][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-06-13 01:09:09.625][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:09.627][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:09.628][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:09.630][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-06-13 01:09:10.230][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:10.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:09:10.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:09:10.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:09:10.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:09:10.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:09:10.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:09:10.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-13 01:09:10.255][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-13 01:09:10.260][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:10.262][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:10.264][rule$waitAsNeeded] Wait 0.053309 second(s).
biodb.TRACE[2024-06-13 01:09:10.323][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:10.632][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:10.634][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:10.636][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:10.638][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:11.233][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:11.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:11.237][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:11.239][rule$waitAsNeeded] Wait 0.083379 second(s).
biodb.TRACE[2024-06-13 01:09:11.326][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:11.630][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:11.632][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:11.634][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:11.637][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:12.219][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:12.222][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:12.224][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:12.226][rule$waitAsNeeded] Wait 0.099164 second(s).
biodb.TRACE[2024-06-13 01:09:12.328][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:12.631][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:12.632][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:12.634][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:12.635][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:13.237][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:13.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:13.242][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:13.244][rule$waitAsNeeded] Wait 0.0836241 second(s).
biodb.TRACE[2024-06-13 01:09:13.346][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:13.643][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:13.644][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:13.646][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:13.647][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:14.240][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:14.242][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:14.244][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:14.246][rule$waitAsNeeded] Wait 0.099364 second(s).
biodb.TRACE[2024-06-13 01:09:14.348][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:14.705][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:14.707][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:14.710][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:14.712][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:15.199][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:15.202][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:15.204][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:15.206][rule$waitAsNeeded] Wait 0.141853 second(s).
biodb.TRACE[2024-06-13 01:09:15.351][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:15.659][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:15.661][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:15.662][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:15.664][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:16.260][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:16.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:16.265][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:16.267][rule$waitAsNeeded] Wait 0.0834291 second(s).
biodb.TRACE[2024-06-13 01:09:16.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:16.665][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:16.668][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:16.670][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:16.672][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:17.271][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:17.273][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:17.276][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:17.278][rule$waitAsNeeded] Wait 0.0749528 second(s).
biodb.TRACE[2024-06-13 01:09:17.371][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:17.667][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:17.669][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:17.671][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:17.673][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:18.265][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:18.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:18.269][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:18.272][rule$waitAsNeeded] Wait 0.098748 second(s).
biodb.TRACE[2024-06-13 01:09:18.389][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:18.689][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:18.691][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:18.693][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:18.695][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:19.275][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-13 01:09:19.278][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-13 01:09:19.280][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-13 01:09:19.282][rule$waitAsNeeded] Wait 0.106217 second(s).
biodb.TRACE[2024-06-13 01:09:19.392][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-13 01:09:19.696][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-06-13 01:09:19.698][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-13 01:09:19.701][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-13 01:09:19.703][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-06-13 01:09:20.301][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-13 01:09:20.304][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2024-06-13 01:09:20.308][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-13 01:09:20.309][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-13 01:09:20.311][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-13 01:09:20.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:09:20.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:09:20.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:09:20.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:09:20.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:09:20.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:09:20.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:09:20.329][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.334][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:09:20.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:09:20.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:09:20.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:09:20.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:09:20.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:09:20.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:09:20.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:09:20.397][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.402][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-13 01:09:20.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-13 01:09:20.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-13 01:09:20.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-13 01:09:20.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-13 01:09:20.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-13 01:09:20.486][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-13 01:09:20.488][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-13 01:09:20.492][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-13 01:09:20.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:09:20.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:09:20.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:09:20.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:09:20.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:09:20.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:09:20.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-13 01:09:20.518][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-06-13 01:09:20.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-13 01:09:20.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:09:20.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:09:20.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:09:20.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:09:20.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:09:20.541][FUN] Functions in observer BiodbConfig: [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[2024-06-13 01:09:20.543][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-06-13 01:09:20.545][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-13 01:09:20.547][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-13 01:09:20.562][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-13 01:09:20.565][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-13 01:09:20.567][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-13 01:09:20.569][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-13 01:09:20.571][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-13 01:09:20.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-13 01:09:20.574][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-13 01:09:20.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-13 01:09:20.578][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-13 01:09:20.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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
LipidmapsStructureConn 3.87 3.89207.02
LipidmapsStructureEntry0.700.020.72