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This page was generated on 2024-05-04 11:37:29 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 2024-05-04 01:04:27 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:08:18 -0400 (Sat, 04 May 2024)
EllapsedTime: 231.2 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 beta (2024-04-15 r86425 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 3.36   2.25   60.71
* 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 beta (2024-04-15 r86425 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 [2024-05-04 01:06:19.512][biodb::testContext]
biodb.INFO [2024-05-04 01:06:19.516][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 01:06:19.517][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-04 01:06:19.519][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 01:06:19.520][biodb::testContext]
biodb.INFO [2024-05-04 01:06:19.528][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 01:06:19.532][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 01:06:19.541][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:06:19.543][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 01:06:19.545][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 01:06:19.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.551][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 01:06:19.585][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 01:06:19.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.590][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 01:06:19.591][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 01:06:19.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.596][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 01:06:19.597][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 01:06:19.598][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 01:06:19.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.603][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 01:06:19.604][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 01:06:19.605][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 01:06:19.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.610][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 01:06:19.611][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 01:06:19.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.616][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 01:06:19.617][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 01:06:19.618][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 01:06:19.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.623][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 01:06:19.624][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 01:06:19.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.628][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[2024-05-04 01:06:19.629][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 01:06:19.630][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 01:06:19.631][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 01:06:19.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.636][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 01:06:19.637][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 01:06:19.638][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 01:06:19.640][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 01:06:19.641][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 01:06:19.642][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 01:06:19.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.646][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[2024-05-04 01:06:19.647][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 01:06:19.648][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 01:06:19.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.653][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 01:06:19.654][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 01:06:19.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.657][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[2024-05-04 01:06:19.659][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 01:06:19.660][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 01:06:19.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.664][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 01:06:19.666][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 01:06:19.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.669][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[2024-05-04 01:06:19.670][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 01:06:19.672][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 01:06:19.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.677][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 01:06:19.678][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 01:06:19.682][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 01:06:19.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.687][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 01:06:19.688][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 01:06:19.689][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 01:06:19.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.696][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 01:06:19.727][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.741][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 01:06:19.743][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.744][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:06:19.745][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.747][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.749][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.750][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:06:19.752][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:06:19.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.754][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 01:06:19.756][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:06:19.757][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.758][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:06:19.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:06:19.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 01:06:19.760][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 01:06:19.760][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 01:06:19.761][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:06:19.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:06:19.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.768][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.770][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.777][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:06:19.778][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:06:19.779][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.780][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.781][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 01:06:19.784][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.785][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 01:06:19.786][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.787][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:06:19.788][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.790][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.791][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.792][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.794][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 01:06:19.795][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:06:19.796][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.797][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 01:06:19.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:06:19.800][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.802][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.803][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:06:19.803][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:06:19.803][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 01:06:19.803][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 01:06:19.803][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 01:06:19.804][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:06:19.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.808][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:06:19.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.811][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.813][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:06:19.815][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:06:19.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.818][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.819][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 01:06:19.821][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.822][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 01:06:19.824][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.825][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:06:19.826][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.827][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.829][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.830][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.831][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:06:19.833][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:06:19.834][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.835][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 01:06:19.837][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:06:19.838][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.839][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.840][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.841][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:06:19.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:06:19.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.850][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:06:19.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:06:19.853][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.855][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.856][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 01:06:19.858][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.860][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 01:06:19.861][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.862][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:06:19.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.865][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.866][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.867][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.868][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 01:06:19.870][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:06:19.871][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.872][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 01:06:19.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:06:19.875][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.876][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:19.877][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.878][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:06:19.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:06:19.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:19.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:19.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:06:19.886][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:06:19.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:06:19.890][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:19.891][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:19.896][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:06:19.897][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.970][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[2024-05-04 01:06:19.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:19.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:19.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:19.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:19.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:19.994][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 01:06:20.003][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 01:06:20.005][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 01:06:20.007][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 01:06:20.010][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 01:06:20.013][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 01:06:20.015][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 01:06:20.016][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 01:06:20.018][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 01:06:20.020][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 01:06:20.023][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 01:06:20.025][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 01:06:20.027][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 01:06:20.029][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 01:06:20.030][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 01:06:20.032][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 01:06:20.033][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 01:06:20.035][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 01:06:20.037][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 01:06:20.038][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 01:06:20.040][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 01:06:20.042][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 01:06:20.043][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 01:06:20.045][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 01:06:20.047][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 01:06:20.048][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 01:06:20.050][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 01:06:20.052][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 01:06:20.053][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 01:06:20.055][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 01:06:20.057][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 01:06:20.059][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 01:06:20.060][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 01:06:20.062][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 01:06:20.063][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 01:06:20.065][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 01:06:20.067][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 01:06:20.068][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 01:06:20.070][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 01:06:20.071][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 01:06:20.073][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 01:06:20.075][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 01:06:20.076][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 01:06:20.078][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 01:06:20.079][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 01:06:20.081][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 01:06:20.084][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 01:06:20.085][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 01:06:20.087][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 01:06:20.089][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 01:06:20.090][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 01:06:20.092][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 01:06:20.093][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 01:06:20.095][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 01:06:20.096][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 01:06:20.098][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 01:06:20.100][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 01:06:20.101][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 01:06:20.103][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 01:06:20.104][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 01:06:20.106][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 01:06:20.107][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 01:06:20.109][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 01:06:20.111][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 01:06:20.112][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 01:06:20.114][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 01:06:20.115][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 01:06:20.117][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 01:06:20.118][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 01:06:20.120][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 01:06:20.122][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 01:06:20.123][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 01:06:20.125][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 01:06:20.126][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 01:06:20.128][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 01:06:20.129][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 01:06:20.131][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 01:06:20.133][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 01:06:20.134][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 01:06:20.136][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 01:06:20.137][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 01:06:20.139][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 01:06:20.140][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 01:06:20.176][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 01:06:20.179][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 01:06:20.182][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:06:20.184][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.186][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.187][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[2024-05-04 01:06:20.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.252][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[2024-05-04 01:06:20.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.260][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[2024-05-04 01:06:20.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.276][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[2024-05-04 01:06:20.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.284][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[2024-05-04 01:06:20.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.292][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[2024-05-04 01:06:20.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.302][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[2024-05-04 01:06:20.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.318][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[2024-05-04 01:06:20.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:20.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:06:20.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.334][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[2024-05-04 01:06:20.336][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-04 01:06:20.346][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:06:20.348][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:20.349][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-04 01:06:20.351][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:20.352][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:06:20.353][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:20.354][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:06:20.355][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:20.357][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:06:20.358][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:06:20.359][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:06:20.361][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:20.362][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-04 01:06:20.363][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-04 01:06:20.364][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-04 01:06:20.365][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 01:06:20.367][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:06:20.367][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:06:20.368][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:06:20.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:20.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:20.372][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:06:20.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:06:20.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:06:20.375][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:06:20.376][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-04 01:06:20.376][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-04 01:06:20.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:06:20.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:06:20.380][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 01:06:20.381][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:06:20.387][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-04 01:06:20.389][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 01:06:20.411][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:06:20.412][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-04 01:06:20.416][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:06:20.420][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-04 01:06:20.424][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-04 01:06:20.425][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-04 01:06:20.427][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-04 01:06:20.429][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-04 01:06:20.439][biodb::testThat]
biodb.INFO [2024-05-04 01:06:20.440][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 01:06:20.441][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:20.443][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:20.450][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[2024-05-04 01:06:20.452][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-04 01:06:20.457][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-04 01:06:20.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:20.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:20.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:20.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:20.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:20.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:20.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:20.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 01:06:20.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 01:06:20.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.545][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:20.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:20.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.550][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:20.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:20.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.556][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:20.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:20.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:20.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:20.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:20.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:20.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.595][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:20.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:20.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.600][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:20.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:20.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.605][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:20.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:20.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.610][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:20.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:20.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.617][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:20.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:20.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.636][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:20.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.642][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-04 01:06:20.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.703][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:20.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:20.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:20.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.793][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:20.838][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-04 01:06:20.854][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 01:06:20.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 01:06:20.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 01:06:20.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 01:06:20.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 01:06:20.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 01:06:20.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.875][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 01:06:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 01:06:20.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:20.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.986][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.991][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:20.996][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:20.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:20.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.044][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.048][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.081][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.084][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.188][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.189][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.191][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.258][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.264][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.265][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.267][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.269][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.300][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.301][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.304][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.326][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.335][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.337][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.339][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.340][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.378][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.380][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.382][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.390][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.391][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.394][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.415][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.416][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.440][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.441][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.444][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.467][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.478][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.481][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.521][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.523][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.526][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:21.539][biodb::testThat]
biodb.INFO [2024-05-04 01:06:21.540][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 01:06:21.541][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:21.543][biodb::testThat]
biodb.DEBUG[2024-05-04 01:06:21.556][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-04 01:06:21.562][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 01:06:21.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-05-04 01:06:21.571][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 01:06:21.575][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-05-04 01:06:21.576][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 01:06:21.600][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-04 01:06:21.602][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-04 01:06:21.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:21.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:21.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:21.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:21.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:21.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:21.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:21.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 01:06:21.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 01:06:21.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 01:06:21.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 01:06:21.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.689][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:21.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:21.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.694][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:21.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:21.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.701][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.706][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:21.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:21.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.722][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:21.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.734][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:21.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:21.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.746][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:21.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:21.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.761][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:21.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.766][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-04 01:06:21.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.782][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:21.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:21.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:21.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:21.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:21.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.831][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:21.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:21.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:21.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:21.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:21.868][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-04 01:06:21.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-04 01:06:21.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-04 01:06:21.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-04 01:06:21.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-04 01:06:21.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:21.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-04 01:06:21.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-04 01:06:21.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:21.911][biodb::testThat]
biodb.INFO [2024-05-04 01:06:21.913][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 01:06:21.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:21.915][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:21.919][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:21.921][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:21.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:21.923][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:21.925][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-04 01:06:21.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:22.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:22.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:22.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:22.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:22.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:22.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:22.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:22.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:22.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:22.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:22.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:22.017][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-04 01:06:22.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-04 01:06:22.041][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:22.043][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:22.045][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-05-04 01:06:22.853][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2024-05-04 01:06:22.855][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:22.857][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:22.859][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-05-04 01:06:23.451][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:06:23.454][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-05-04 01:06:23.470][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-05-04 01:06:23.473][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-04 01:06:23.519][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:23.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:23.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.523][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:23.538][biodb::testThat]
biodb.INFO [2024-05-04 01:06:23.540][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 01:06:23.541][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:23.542][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:23.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:23.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:23.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:23.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:23.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:23.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:23.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:23.708][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-04 01:06:23.712][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 01:06:23.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-04 01:06:23.729][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 01:06:23.734][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-04 01:06:23.784][biodb::testThat]
biodb.INFO [2024-05-04 01:06:23.786][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 01:06:23.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:23.788][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:23.820][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.826][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.831][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 01:06:23.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 01:06:23.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 01:06:23.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 01:06:23.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.893][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 01:06:23.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 01:06:23.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 01:06:23.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:23.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 01:06:23.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 01:06:23.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:23.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:23.933][biodb::testThat]
biodb.INFO [2024-05-04 01:06:23.934][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 01:06:23.936][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:23.937][biodb::testThat]
biodb.INFO [2024-05-04 01:06:23.960][biodb::testThat]
biodb.INFO [2024-05-04 01:06:23.961][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 01:06:23.963][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:23.964][biodb::testThat]
biodb.INFO [2024-05-04 01:06:23.985][biodb::testThat]
biodb.INFO [2024-05-04 01:06:23.987][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 01:06:23.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:23.989][biodb::testThat]
biodb.DEBUG[2024-05-04 01:06:23.995][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-04 01:06:24.280][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-04 01:06:25.119][biodb::testThat]
biodb.INFO [2024-05-04 01:06:25.121][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 01:06:25.123][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:25.125][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:25.148][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:25.151][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:25.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.155][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.158][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.160][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:25.163][biodb::testThat]
biodb.INFO [2024-05-04 01:06:25.164][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-04 01:06:25.165][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:25.166][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:25.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:25.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:25.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:25.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.208][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:25.320][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-04 01:06:25.327][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 01:06:25.330][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-04 01:06:25.333][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 01:06:25.335][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-04 01:06:25.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-04 01:06:25.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 01:06:25.423][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-04 01:06:25.425][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 01:06:25.428][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-04 01:06:25.463][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 01:06:25.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 01:06:25.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:25.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:25.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:25.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:25.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:25.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:25.547][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-04 01:06:25.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:25.565][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:25.580][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-04 01:06:25.864][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[2024-05-04 01:06:25.865][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:25.867][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[2024-05-04 01:06:25.869][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[2024-05-04 01:06:31.218][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:06:31.223][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-05-04 01:06:31.392][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-05-04 01:06:33.533][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-04 01:06:33.537][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:33.539][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:33.542][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-05-04 01:06:33.837][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2024-05-04 01:06:33.839][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:33.843][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:33.846][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-05-04 01:06:34.439][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:06:34.442][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-05-04 01:06:34.449][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-05-04 01:06:34.551][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-05-04 01:06:34.559][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:34.562][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:34.566][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-05-04 01:06:34.864][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[2024-05-04 01:06:34.865][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:34.868][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[2024-05-04 01:06:34.870][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[2024-05-04 01:06:35.455][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:06:35.460][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-05-04 01:06:35.469][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-05-04 01:06:35.526][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:35.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:35.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:35.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:35.568][biodb::testThat]
biodb.INFO [2024-05-04 01:06:35.569][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-04 01:06:35.571][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:35.572][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 01:06:35.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 01:06:35.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:35.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:35.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:35.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:35.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:35.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:35.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:35.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:35.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:35.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:35.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:35.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:35.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:35.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:35.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:35.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:35.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:35.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:35.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:35.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:35.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:35.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:35.658][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-04 01:06:35.662][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:35.664][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:35.667][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-05-04 01:06:35.955][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2024-05-04 01:06:35.957][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:35.959][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:35.961][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-05-04 01:06:41.489][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:06:41.492][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-05-04 01:06:41.609][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-05-04 01:06:43.320][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-04 01:06:43.374][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 01:06:43.376][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-04 01:06:43.378][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-05-04 01:06:43.395][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-05-04 01:06:43.397][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 01:06:43.400][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-04 01:06:43.402][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 01:06:43.404][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 01:06:43.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:43.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:43.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:43.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:43.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:43.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:43.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:43.439][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-05-04 01:06:43.444][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:43.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:43.449][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-05-04 01:06:43.740][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:06:43.742][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:43.744][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:43.746][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-05-04 01:06:44.335][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:06:44.339][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-05-04 01:06:44.346][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-05-04 01:06:44.353][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-05-04 01:06:44.356][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 01:06:44.359][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-04 01:06:44.362][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-04 01:06:44.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:44.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:44.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:44.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:44.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:44.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:44.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:44.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 01:06:44.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 01:06:44.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 01:06:44.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 01:06:44.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.440][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:44.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:44.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:44.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:44.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.459][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.467][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.484][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.493][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:44.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:44.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.502][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:44.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:44.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.510][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:44.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:44.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.519][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:44.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:44.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:44.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:44.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:44.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:44.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.546][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:44.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:44.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.554][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-04 01:06:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:44.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:44.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:44.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:44.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:44.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.582][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:44.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:44.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.591][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:44.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:44.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.599][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:44.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:44.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.617][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:44.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:44.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:44.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:44.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:44.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:44.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:44.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:44.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:44.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:44.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:44.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:44.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 01:06:44.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 01:06:44.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.931][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:44.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-04 01:06:44.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.940][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:44.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 01:06:44.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.948][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.958][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 01:06:44.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 01:06:44.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.987][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:44.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:44.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:44.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:44.995][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 01:06:44.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:44.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.003][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:45.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:45.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 01:06:45.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 01:06:45.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:45.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:45.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:45.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.037][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:45.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.050][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-04 01:06:45.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:45.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:45.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:45.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:06:45.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:45.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.101][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-04 01:06:45.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:06:45.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.106][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.111][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.121][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:06:45.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:06:45.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:45.171][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-04 01:06:45.180][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 01:06:45.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:45.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:45.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:45.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:45.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:45.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:45.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:45.197][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.202][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.207][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.208][private$selectFields]
biodb.TRACE[2024-05-04 01:06:45.209][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:45.210][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:45.211][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.213][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.214][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.216][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.218][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.219][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.221][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.223][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.224][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.225][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.227][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.229][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.230][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:45.232][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.237][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.242][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-04 01:06:45.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:45.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:45.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:45.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:45.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:45.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:45.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:45.271][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.281][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.282][private$selectFields]
biodb.TRACE[2024-05-04 01:06:45.283][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:45.284][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:45.286][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.287][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.288][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.292][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.293][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.296][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.297][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.299][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.301][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.303][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.306][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.308][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:45.310][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.317][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.331][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-04 01:06:45.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:45.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:45.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:45.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:45.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:45.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:45.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:45.358][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.364][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.369][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.370][private$selectFields]
biodb.TRACE[2024-05-04 01:06:45.371][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:45.372][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:45.373][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.375][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.376][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.378][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.379][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.381][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.383][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.384][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.386][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:45.387][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.388][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.391][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.392][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:45.393][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.398][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.403][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:45.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.409][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-04 01:06:45.410][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 01:06:45.411][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 01:06:45.433][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:45.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:45.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:45.459][biodb::testThat]
biodb.INFO [2024-05-04 01:06:45.460][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-04 01:06:45.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:45.463][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:45.467][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 01:06:45.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 01:06:45.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:45.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:45.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:45.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:45.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:45.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:45.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:45.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:45.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:45.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:45.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:45.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:45.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:45.592][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-05-04 01:06:45.596][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:45.597][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:45.599][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-05-04 01:06:45.883][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[2024-05-04 01:06:45.885][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:45.887][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[2024-05-04 01:06:45.889][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[2024-05-04 01:06:51.062][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:06:51.066][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-05-04 01:06:51.164][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-05-04 01:06:53.163][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 01:06:53.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:53.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:53.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:53.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:53.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:53.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:53.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:53.239][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.245][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.273][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.275][private$selectFields]
biodb.TRACE[2024-05-04 01:06:53.278][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:53.279][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:53.281][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.283][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.284][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.287][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.288][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.290][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.292][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.293][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.304][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.306][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.307][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.311][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:53.312][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.317][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.322][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.328][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-04 01:06:53.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:53.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:53.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:53.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:53.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:53.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:53.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:53.346][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.354][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.363][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.365][private$selectFields]
biodb.TRACE[2024-05-04 01:06:53.368][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:53.370][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:53.372][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.375][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.377][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.381][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.384][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.386][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.391][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.393][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.394][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.396][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.397][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.400][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.401][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:53.402][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.413][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.418][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-04 01:06:53.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:53.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:53.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:53.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:53.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:53.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:53.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:53.439][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.444][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.450][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.451][private$selectFields]
biodb.TRACE[2024-05-04 01:06:53.452][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:53.453][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:53.455][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.456][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.457][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.460][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.461][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.462][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.465][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.466][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.467][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:53.469][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.470][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.473][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.474][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:53.476][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:53.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.492][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-04 01:06:53.493][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 01:06:53.494][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 01:06:53.522][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:53.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:53.536][biodb::testThat]
biodb.INFO [2024-05-04 01:06:53.537][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-04 01:06:53.539][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:53.540][biodb::testThat]
biodb.TRACE[2024-05-04 01:06:53.544][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 01:06:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 01:06:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:53.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 01:06:53.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:53.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:06:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:53.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:06:53.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:53.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:53.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:53.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:53.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:53.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:53.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:53.653][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-04 01:06:53.657][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 01:06:53.659][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-04 01:06:53.661][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 01:06:53.797][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-04 01:06:55.888][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 01:06:55.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:55.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:55.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:55.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:55.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:55.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:55.939][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.TRACE[2024-05-04 01:06:55.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:55.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:55.947][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:55.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:55.952][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:55.953][private$selectFields]
biodb.TRACE[2024-05-04 01:06:55.954][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:55.956][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:55.957][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:55.958][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.960][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:55.962][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:55.963][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.965][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:55.967][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:55.969][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:55.970][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:55.971][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.973][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:55.977][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:55.979][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:55.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:55.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:55.989][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:55.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:55.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.010][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-04 01:06:56.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:56.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:56.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:56.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:56.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:56.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:56.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:56.041][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.047][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.056][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.058][private$selectFields]
biodb.TRACE[2024-05-04 01:06:56.060][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:56.061][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:56.062][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.064][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.066][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.069][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.071][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.072][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.074][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.076][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.077][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.078][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.079][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.082][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.083][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:56.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.100][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-04 01:06:56.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:56.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:56.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:56.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:56.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:56.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:56.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:06:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.135][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.143][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.145][private$selectFields]
biodb.TRACE[2024-05-04 01:06:56.146][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 01:06:56.148][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 01:06:56.150][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.152][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.154][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.158][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.160][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.162][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.166][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.168][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.170][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-04 01:06:56.172][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.174][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.178][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.180][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-04 01:06:56.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.191][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.199][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:06:56.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:06:56.207][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-04 01:06:56.210][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 01:06:56.211][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 01:06:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:56.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 01:06:56.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:06:56.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 01:06:56.279][biodb::testThat]
biodb.INFO [2024-05-04 01:06:56.280][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-04 01:06:56.282][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:06:56.283][biodb::testThat]
biodb.DEBUG[2024-05-04 01:06:56.285][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-04 01:06:56.286][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 01:06:56.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-04 01:06:56.290][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 01:06:56.291][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 01:06:56.293][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 01:06:56.294][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-04 01:06:56.295][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 01:06:56.297][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 01:06:56.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:06:56.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:06:56.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:06:56.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:06:56.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:06:56.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:06:56.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:06:56.336][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-05-04 01:06:56.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:56.343][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:06:56.346][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:06:56.637][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:06:56.639][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:56.640][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:56.642][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:06:57.234][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:06:57.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:57.237][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:06:57.239][rule$waitAsNeeded] Wait 0.106303 second(s).
biodb.TRACE[2024-05-04 01:06:57.358][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:06:57.646][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:06:57.648][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:57.649][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:57.651][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:06:58.235][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:06:58.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:58.239][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:06:58.240][rule$waitAsNeeded] Wait 0.117545 second(s).
biodb.TRACE[2024-05-04 01:06:58.374][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:06:58.658][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:06:58.659][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:58.660][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:58.662][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:06:59.252][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:06:59.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:06:59.257][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:06:59.259][rule$waitAsNeeded] Wait 0.115345 second(s).
biodb.TRACE[2024-05-04 01:06:59.390][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:06:59.672][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:06:59.675][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:06:59.676][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:06:59.678][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:07:00.268][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:00.270][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:00.272][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:00.274][rule$waitAsNeeded] Wait 0.115848 second(s).
biodb.TRACE[2024-05-04 01:07:00.407][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:07:00.695][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:00.696][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:00.698][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:00.699][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:07:01.284][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:01.285][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:01.286][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:01.288][rule$waitAsNeeded] Wait 0.118107 second(s).
biodb.TRACE[2024-05-04 01:07:01.423][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:07:01.711][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:01.712][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:01.714][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:01.715][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:07:02.299][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:02.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:02.302][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:02.304][rule$waitAsNeeded] Wait 0.118526 second(s).
biodb.TRACE[2024-05-04 01:07:02.439][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:07:02.723][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:02.725][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:02.726][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:02.727][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:07:03.316][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:03.319][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:03.321][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:03.324][rule$waitAsNeeded] Wait 0.11513 second(s).
biodb.TRACE[2024-05-04 01:07:03.455][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:07:03.780][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:03.782][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:03.783][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:03.785][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:07:04.363][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:04.365][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:04.366][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:04.368][rule$waitAsNeeded] Wait 0.0866671 second(s).
biodb.TRACE[2024-05-04 01:07:04.472][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:07:04.759][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:04.761][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:04.763][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:04.765][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:07:05.348][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:05.351][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:05.353][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:05.355][rule$waitAsNeeded] Wait 0.115969 second(s).
biodb.TRACE[2024-05-04 01:07:05.487][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-05-04 01:07:05.771][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:05.772][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:05.774][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:05.775][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-05-04 01:07:06.365][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-05-04 01:07:06.369][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-05-04 01:07:06.371][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 01:07:06.373][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-04 01:07:06.374][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-04 01:07:06.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:07:06.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:06.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:06.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:06.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:06.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:06.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:07:06.404][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:06.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:06.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:06.409][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:06.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:06.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:06.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:06.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:06.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:06.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:06.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:06.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:06.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:06.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:06.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:06.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:06.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:06.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:06.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:06.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:06.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:06.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:06.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:06.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:06.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:07:06.445][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-04 01:07:06.446][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-04 01:07:06.479][biodb::testThat]
biodb.INFO [2024-05-04 01:07:06.480][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-04 01:07:06.482][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:06.483][biodb::testThat]
biodb.DEBUG[2024-05-04 01:07:06.497][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-04 01:07:06.498][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-04 01:07:06.500][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 01:07:06.503][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-04 01:07:06.505][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-04 01:07:06.506][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 01:07:06.508][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 01:07:06.509][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-04 01:07:06.511][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 01:07:06.512][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 01:07:06.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:07:06.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:06.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:06.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:06.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:06.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:06.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:06.539][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-05-04 01:07:06.543][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:06.545][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:07:06.547][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:06.836][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:06.837][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:06.839][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:06.840][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:07.432][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:07.433][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:07.434][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:07.436][rule$waitAsNeeded] Wait 0.110933 second(s).
biodb.TRACE[2024-05-04 01:07:07.555][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:07.847][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:07.849][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:07.852][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:07.854][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:08.448][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:08.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:08.450][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:08.452][rule$waitAsNeeded] Wait 0.103176 second(s).
biodb.TRACE[2024-05-04 01:07:08.572][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:08.857][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:08.860][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:08.862][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:08.863][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:09.449][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:09.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:09.452][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:09.453][rule$waitAsNeeded] Wait 0.117914 second(s).
biodb.TRACE[2024-05-04 01:07:09.588][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:09.873][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:09.874][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:09.876][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:09.877][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:10.465][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:10.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:10.470][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:10.473][rule$waitAsNeeded] Wait 0.115334 second(s).
biodb.TRACE[2024-05-04 01:07:10.604][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:10.892][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:10.894][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:10.895][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:10.896][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:11.481][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:11.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:11.486][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:11.488][rule$waitAsNeeded] Wait 0.115485 second(s).
biodb.TRACE[2024-05-04 01:07:11.620][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:11.912][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:11.914][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:11.916][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:11.919][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:12.513][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:12.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:12.517][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:12.518][rule$waitAsNeeded] Wait 0.101343 second(s).
biodb.TRACE[2024-05-04 01:07:12.636][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:12.924][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:12.926][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:12.928][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:12.930][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:13.514][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:13.516][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:13.518][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:13.520][rule$waitAsNeeded] Wait 0.115779 second(s).
biodb.TRACE[2024-05-04 01:07:13.653][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:13.950][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:13.952][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:13.954][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:13.956][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:14.545][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:14.548][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:14.550][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:14.552][rule$waitAsNeeded] Wait 0.0999491 second(s).
biodb.TRACE[2024-05-04 01:07:14.669][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:14.962][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:14.963][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:14.965][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:14.966][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:15.561][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:15.562][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:15.564][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:15.566][rule$waitAsNeeded] Wait 0.101899 second(s).
biodb.TRACE[2024-05-04 01:07:15.685][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-05-04 01:07:15.971][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:15.972][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:15.974][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:15.975][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-05-04 01:07:16.562][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:16.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:07:16.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:16.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:16.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:16.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:16.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:16.588][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[2024-05-04 01:07:16.591][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.INFO [2024-05-04 01:07:16.596][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2024-05-04 01:07:16.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:16.601][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:16.604][rule$waitAsNeeded] Wait 0.0809541 second(s).
biodb.TRACE[2024-05-04 01:07:16.701][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:16.988][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:16.992][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:16.993][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:16.995][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:17.782][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:17.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:17.786][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:07:17.789][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:18.079][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:18.081][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:18.082][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:18.084][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:18.673][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:18.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:18.677][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:18.680][rule$waitAsNeeded] Wait 0.109407 second(s).
biodb.TRACE[2024-05-04 01:07:18.795][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:19.080][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:19.082][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:19.083][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:19.085][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:19.673][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:19.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:19.676][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:19.678][rule$waitAsNeeded] Wait 0.117044 second(s).
biodb.TRACE[2024-05-04 01:07:19.811][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:20.097][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:20.098][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:20.100][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:20.101][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:20.689][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:20.692][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:20.694][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:20.696][rule$waitAsNeeded] Wait 0.115509 second(s).
biodb.TRACE[2024-05-04 01:07:20.828][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:21.116][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:21.117][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:21.119][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:21.120][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:21.705][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:21.707][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:21.710][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:21.712][rule$waitAsNeeded] Wait 0.115649 second(s).
biodb.TRACE[2024-05-04 01:07:21.844][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:22.130][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:22.132][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:22.135][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:22.138][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:22.721][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:22.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:22.726][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:22.728][rule$waitAsNeeded] Wait 0.115655 second(s).
biodb.TRACE[2024-05-04 01:07:22.860][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:23.152][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:23.154][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:23.155][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:23.157][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:23.737][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:23.740][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:23.743][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:23.745][rule$waitAsNeeded] Wait 0.115025 second(s).
biodb.TRACE[2024-05-04 01:07:23.876][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:24.169][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:24.171][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:24.173][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:24.175][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:24.769][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:24.772][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:24.790][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:24.795][rule$waitAsNeeded] Wait 0.0802779 second(s).
biodb.TRACE[2024-05-04 01:07:24.892][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:25.184][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:25.186][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:25.187][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:25.188][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:25.785][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:25.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:25.790][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:25.792][rule$waitAsNeeded] Wait 0.099709 second(s).
biodb.TRACE[2024-05-04 01:07:25.909][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-05-04 01:07:26.208][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:26.209][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:26.211][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:26.217][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-05-04 01:07:26.801][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.INFO [2024-05-04 01:07:26.806][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-05-04 01:07:26.810][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-05-04 01:07:26.815][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 01:07:26.818][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-04 01:07:26.821][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-04 01:07:26.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:07:26.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:26.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:26.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:26.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:26.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:26.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:07:26.868][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.874][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:07:26.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:07:26.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:26.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:26.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:26.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:26.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:26.925][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.TRACE[2024-05-04 01:07:26.928][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:07:26.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:26.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:07:26.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:07:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:26.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:07:26.998][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-04 01:07:26.999][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 01:07:27.000][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-04 01:07:27.480][biodb::testThat]
biodb.INFO [2024-05-04 01:07:27.482][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-04 01:07:27.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:27.487][biodb::testThat]
biodb.INFO [2024-05-04 01:07:27.595][biodb::testThat]
biodb.INFO [2024-05-04 01:07:27.597][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-04 01:07:27.599][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:27.601][biodb::testThat]
biodb.INFO [2024-05-04 01:07:27.625][biodb::testThat]
biodb.INFO [2024-05-04 01:07:27.627][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-04 01:07:27.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:27.629][biodb::testThat]
biodb.DEBUG[2024-05-04 01:07:27.633][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-04 01:07:27.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:27.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:07:27.641][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-05-04 01:07:27.932][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV does not exist.
biodb.TRACE[2024-05-04 01:07:27.934][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:27.937][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:27.964][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-05-04 01:07:33.315][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:07:33.318][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-05-04 01:07:33.652][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-05-04 01:07:35.761][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 01:07:35.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 01:07:35.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:35.768][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:07:35.769][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:07:35.771][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 01:07:35.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:07:35.775][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 01:07:35.778][biodb::testThat]
biodb.INFO [2024-05-04 01:07:35.780][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-04 01:07:35.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:35.783][biodb::testThat]
biodb.ERROR[2024-05-04 01:07:35.802][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-04 01:07:35.822][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-04 01:07:35.839][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 01:07:35.841][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-04 01:07:35.843][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-04 01:07:35.844][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 01:07:35.845][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:35.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:35.848][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:35.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:35.850][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-04 01:07:35.863][biodb::testContext]
biodb.INFO [2024-05-04 01:07:35.865][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 01:07:35.866][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-04 01:07:35.867][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 01:07:35.869][biodb::testContext]
biodb.INFO [2024-05-04 01:07:35.872][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 01:07:35.874][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 01:07:35.881][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:07:35.882][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 01:07:35.883][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 01:07:35.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.888][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 01:07:35.890][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 01:07:35.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.894][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 01:07:35.896][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 01:07:35.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.901][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 01:07:35.902][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 01:07:35.903][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 01:07:35.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.908][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 01:07:35.909][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 01:07:35.911][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 01:07:35.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.916][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 01:07:35.917][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 01:07:35.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.922][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 01:07:35.923][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 01:07:35.924][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 01:07:35.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.929][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 01:07:35.930][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 01:07:35.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.935][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 01:07:35.936][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 01:07:35.938][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 01:07:35.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.943][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 01:07:35.944][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 01:07:35.945][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 01:07:35.947][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 01:07:35.948][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 01:07:35.950][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 01:07:35.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.954][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 01:07:35.956][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 01:07:35.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.961][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 01:07:35.962][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 01:07:35.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.967][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 01:07:35.968][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 01:07:35.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.973][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 01:07:35.974][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 01:07:35.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.979][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 01:07:35.980][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 01:07:35.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:35.987][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 01:07:35.989][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 01:07:35.995][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 01:07:35.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:35.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:35.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.000][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 01:07:36.001][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 01:07:36.003][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 01:07:36.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.008][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 01:07:36.010][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.011][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 01:07:36.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:36.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.018][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.019][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.020][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:07:36.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:36.023][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.024][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 01:07:36.025][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:36.027][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.028][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.029][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:07:36.029][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:07:36.029][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 01:07:36.029][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 01:07:36.029][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 01:07:36.030][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:36.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.034][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:36.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.039][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:36.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:36.043][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.044][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.045][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 01:07:36.047][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.049][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 01:07:36.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.051][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:36.052][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.055][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.056][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.057][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 01:07:36.058][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:36.060][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.061][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 01:07:36.062][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:36.063][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.065][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.066][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:07:36.066][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:07:36.066][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 01:07:36.066][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 01:07:36.066][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 01:07:36.067][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:36.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:36.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.075][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.076][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.077][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:36.078][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:36.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.083][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.084][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 01:07:36.087][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.089][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 01:07:36.091][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.093][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:36.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.098][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.100][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.102][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.104][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:07:36.105][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:36.107][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.109][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 01:07:36.110][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:36.111][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.113][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.114][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.115][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:36.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.119][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:36.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.124][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:36.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:36.148][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.150][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.151][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 01:07:36.153][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.155][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 01:07:36.156][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.157][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:36.159][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.160][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.161][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.162][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.164][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 01:07:36.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:36.166][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.168][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 01:07:36.169][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:36.171][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.173][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.174][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.175][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:36.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.179][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:36.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.183][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.185][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:36.186][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:36.187][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.188][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.190][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:07:36.191][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.209][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[2024-05-04 01:07:36.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.226][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[2024-05-04 01:07:36.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.253][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[2024-05-04 01:07:36.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.287][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[2024-05-04 01:07:36.288][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 01:07:36.290][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 01:07:36.292][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 01:07:36.293][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 01:07:36.295][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 01:07:36.296][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 01:07:36.298][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 01:07:36.300][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 01:07:36.301][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 01:07:36.303][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 01:07:36.304][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 01:07:36.306][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 01:07:36.308][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 01:07:36.309][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 01:07:36.311][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 01:07:36.312][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 01:07:36.314][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 01:07:36.316][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 01:07:36.317][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 01:07:36.319][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 01:07:36.321][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 01:07:36.322][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 01:07:36.324][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 01:07:36.325][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 01:07:36.327][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 01:07:36.329][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 01:07:36.330][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 01:07:36.332][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 01:07:36.333][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 01:07:36.335][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 01:07:36.337][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 01:07:36.338][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 01:07:36.340][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 01:07:36.341][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 01:07:36.343][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 01:07:36.345][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 01:07:36.346][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 01:07:36.348][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 01:07:36.349][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 01:07:36.351][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 01:07:36.352][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 01:07:36.354][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 01:07:36.356][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 01:07:36.357][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 01:07:36.359][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 01:07:36.360][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 01:07:36.362][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 01:07:36.364][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 01:07:36.365][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 01:07:36.367][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 01:07:36.368][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 01:07:36.370][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 01:07:36.372][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 01:07:36.373][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 01:07:36.375][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 01:07:36.376][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 01:07:36.378][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 01:07:36.380][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 01:07:36.381][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 01:07:36.383][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 01:07:36.384][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 01:07:36.386][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 01:07:36.387][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 01:07:36.389][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 01:07:36.391][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 01:07:36.392][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 01:07:36.394][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 01:07:36.396][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 01:07:36.397][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 01:07:36.399][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 01:07:36.400][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 01:07:36.402][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 01:07:36.403][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 01:07:36.405][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 01:07:36.407][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 01:07:36.408][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 01:07:36.410][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 01:07:36.412][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 01:07:36.413][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 01:07:36.415][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 01:07:36.416][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 01:07:36.418][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 01:07:36.420][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 01:07:36.421][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 01:07:36.424][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 01:07:36.425][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:07:36.426][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.429][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.506][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[2024-05-04 01:07:36.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.530][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[2024-05-04 01:07:36.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:36.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:36.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:36.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:36.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:36.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:36.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:36.577][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[2024-05-04 01:07:36.579][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-04 01:07:36.581][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:07:36.583][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.585][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.586][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.587][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:36.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.590][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.591][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.592][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.593][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:07:36.595][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:36.596][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.597][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-04 01:07:36.598][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-04 01:07:36.599][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-04 01:07:36.601][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:36.602][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:07:36.602][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:07:36.603][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:36.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.607][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:36.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:36.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:36.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:36.611][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-04 01:07:36.611][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-04 01:07:36.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:36.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:36.615][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:36.616][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:36.618][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-04 01:07:36.619][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 01:07:36.623][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:07:36.624][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-04 01:07:36.625][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:07:36.627][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-04 01:07:36.629][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-04 01:07:36.630][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-04 01:07:36.632][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-04 01:07:36.633][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-04 01:07:36.635][biodb::testThat]
biodb.INFO [2024-05-04 01:07:36.636][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-04 01:07:36.638][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:36.639][biodb::testThat]
biodb.DEBUG[2024-05-04 01:07:36.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-05-04 01:07:36.649][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:36.650][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:07:36.652][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-05-04 01:07:36.935][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[2024-05-04 01:07:36.937][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:36.938][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[2024-05-04 01:07:36.941][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[2024-05-04 01:07:37.525][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:07:37.529][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-05-04 01:07:37.536][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-05-04 01:07:37.558][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-05-04 01:07:37.562][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:37.564][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:37.565][rule$waitAsNeeded] Wait 0.0859711 second(s).
biodb.TRACE[2024-05-04 01:07:37.663][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-05-04 01:07:37.956][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[2024-05-04 01:07:37.959][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:37.962][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[2024-05-04 01:07:37.965][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[2024-05-04 01:07:38.559][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:07:38.563][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-05-04 01:07:38.571][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-05-04 01:07:38.598][biodb::testThat]
biodb.INFO [2024-05-04 01:07:38.600][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-04 01:07:38.601][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:38.604][biodb::testThat]
biodb.INFO [2024-05-04 01:07:38.646][biodb::testThat]
biodb.INFO [2024-05-04 01:07:38.648][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-04 01:07:38.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:38.650][biodb::testThat]
biodb.DEBUG[2024-05-04 01:07:38.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-04 01:07:38.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:38.659][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:38.660][rule$waitAsNeeded] Wait 0.00188899 second(s).
biodb.TRACE[2024-05-04 01:07:38.667][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-05-04 01:07:38.951][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2024-05-04 01:07:38.952][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:38.954][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[2024-05-04 01:07:38.956][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-05-04 01:07:39.360][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:07:39.363][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-05-04 01:07:39.372][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-05-04 01:07:39.383][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-05-04 01:07:39.390][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 01:07:39.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-04 01:07:39.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 01:07:39.399][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-04 01:07:39.406][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-05-04 01:07:39.410][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:39.412][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:39.413][rule$waitAsNeeded] Wait 0.253157 second(s).
biodb.TRACE[2024-05-04 01:07:39.674][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-05-04 01:07:39.970][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[2024-05-04 01:07:39.973][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:40.002][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[2024-05-04 01:07:40.006][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[2024-05-04 01:07:40.415][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:07:40.419][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-05-04 01:07:40.425][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-05-04 01:07:40.434][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-05-04 01:07:40.440][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:40.442][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:40.445][rule$waitAsNeeded] Wait 0.227793 second(s).
biodb.TRACE[2024-05-04 01:07:40.692][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-05-04 01:07:40.980][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2024-05-04 01:07:40.981][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:40.983][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[2024-05-04 01:07:40.985][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-05-04 01:07:42.415][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:07:42.418][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-05-04 01:07:42.436][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-05-04 01:07:42.652][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-05-04 01:07:42.656][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:42.657][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:07:42.660][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-05-04 01:07:42.949][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6 does not exist.
biodb.TRACE[2024-05-04 01:07:42.951][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:42.954][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:42.958][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-05-04 01:07:44.521][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 01:07:44.527][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-05-04 01:07:44.555][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-05-04 01:07:44.806][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 01:07:44.808][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-04 01:07:44.809][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-04 01:07:44.811][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 01:07:44.812][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:44.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:44.814][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:44.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:44.817][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-04 01:07:44.823][biodb::testContext]
biodb.INFO [2024-05-04 01:07:44.824][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 01:07:44.825][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-04 01:07:44.826][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 01:07:44.827][biodb::testContext]
biodb.INFO [2024-05-04 01:07:44.831][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 01:07:44.833][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 01:07:44.839][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:07:44.840][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 01:07:44.842][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 01:07:44.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.846][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 01:07:44.848][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 01:07:44.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.852][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 01:07:44.854][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 01:07:44.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.857][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[2024-05-04 01:07:44.858][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 01:07:44.859][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 01:07:44.861][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 01:07:44.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.865][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 01:07:44.866][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 01:07:44.868][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 01:07:44.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.871][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[2024-05-04 01:07:44.872][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 01:07:44.873][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 01:07:44.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.878][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 01:07:44.879][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 01:07:44.881][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 01:07:44.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.884][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[2024-05-04 01:07:44.885][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 01:07:44.886][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 01:07:44.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.891][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 01:07:44.892][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 01:07:44.893][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 01:07:44.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.898][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 01:07:44.899][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 01:07:44.901][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 01:07:44.903][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 01:07:44.905][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 01:07:44.906][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 01:07:44.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.911][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 01:07:44.912][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 01:07:44.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.916][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 01:07:44.918][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 01:07:44.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.922][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 01:07:44.924][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 01:07:44.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.928][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 01:07:44.930][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 01:07:44.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.934][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 01:07:44.936][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 01:07:44.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.939][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[2024-05-04 01:07:44.941][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 01:07:44.942][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 01:07:44.946][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 01:07:44.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:44.950][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 01:07:44.952][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 01:07:44.953][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 01:07:44.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:44.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:44.957][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[2024-05-04 01:07:44.958][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 01:07:44.960][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:44.961][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 01:07:44.962][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:44.964][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:44.965][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:44.966][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:44.968][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:44.969][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:44.970][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:07:44.971][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:44.973][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:44.975][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 01:07:44.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:44.979][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:44.981][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:44.983][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:07:44.983][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:07:44.983][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 01:07:44.983][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 01:07:44.983][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 01:07:44.985][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:44.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:44.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:44.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:44.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:44.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:44.994][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:44.996][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:44.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:44.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:44.999][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.000][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.002][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 01:07:45.004][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.006][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 01:07:45.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.008][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:45.009][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.010][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.012][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.013][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.014][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 01:07:45.015][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:45.017][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.018][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 01:07:45.019][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:45.020][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.022][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.023][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:07:45.023][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:07:45.023][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 01:07:45.023][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 01:07:45.023][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 01:07:45.024][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:45.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:45.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.033][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.034][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:45.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:45.036][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.037][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.039][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 01:07:45.041][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.042][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 01:07:45.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.045][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:45.046][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.048][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.049][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.050][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.052][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:07:45.053][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:45.055][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.056][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 01:07:45.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:45.058][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.060][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.061][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:45.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.065][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:45.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.070][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:45.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:45.074][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.091][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.093][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 01:07:45.095][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.097][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 01:07:45.098][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.100][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:45.102][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.103][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.104][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.106][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 01:07:45.108][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:45.109][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.110][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 01:07:45.111][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:45.113][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.114][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.115][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.116][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:45.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:45.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.124][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.126][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:45.127][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:45.128][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.129][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.131][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:07:45.132][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.161][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.DEBUG[2024-05-04 01:07:45.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.172][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[2024-05-04 01:07:45.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.195][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[2024-05-04 01:07:45.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.217][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[2024-05-04 01:07:45.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.230][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 01:07:45.231][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 01:07:45.233][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 01:07:45.235][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 01:07:45.236][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 01:07:45.238][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 01:07:45.239][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 01:07:45.241][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 01:07:45.243][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 01:07:45.244][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 01:07:45.246][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 01:07:45.247][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 01:07:45.249][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 01:07:45.250][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 01:07:45.252][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 01:07:45.254][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 01:07:45.255][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 01:07:45.257][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 01:07:45.258][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 01:07:45.260][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 01:07:45.262][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 01:07:45.263][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 01:07:45.265][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 01:07:45.266][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 01:07:45.268][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 01:07:45.270][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 01:07:45.271][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 01:07:45.273][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 01:07:45.275][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 01:07:45.276][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 01:07:45.278][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 01:07:45.280][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 01:07:45.281][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 01:07:45.283][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 01:07:45.284][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 01:07:45.286][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 01:07:45.288][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 01:07:45.289][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 01:07:45.291][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 01:07:45.292][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 01:07:45.294][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 01:07:45.295][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 01:07:45.297][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 01:07:45.299][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 01:07:45.300][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 01:07:45.302][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 01:07:45.304][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 01:07:45.305][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 01:07:45.307][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 01:07:45.308][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 01:07:45.310][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 01:07:45.312][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 01:07:45.313][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 01:07:45.315][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 01:07:45.317][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 01:07:45.320][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 01:07:45.323][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 01:07:45.325][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 01:07:45.328][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 01:07:45.331][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 01:07:45.334][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 01:07:45.337][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 01:07:45.339][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 01:07:45.342][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 01:07:45.345][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 01:07:45.348][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 01:07:45.351][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 01:07:45.353][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 01:07:45.354][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 01:07:45.356][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 01:07:45.358][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 01:07:45.359][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 01:07:45.361][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 01:07:45.362][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 01:07:45.364][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 01:07:45.366][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 01:07:45.368][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 01:07:45.369][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 01:07:45.371][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 01:07:45.373][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 01:07:45.374][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 01:07:45.376][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 01:07:45.377][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 01:07:45.379][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 01:07:45.381][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 01:07:45.383][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 01:07:45.384][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.386][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.530][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[2024-05-04 01:07:45.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 01:07:45.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:45.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:45.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:45.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:45.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:45.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:45.543][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-04 01:07:45.546][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:07:45.549][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.551][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 01:07:45.556][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.559][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.561][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.563][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.565][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 01:07:45.567][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 01:07:45.568][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.570][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-04 01:07:45.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-04 01:07:45.572][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-04 01:07:45.574][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 01:07:45.575][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 01:07:45.575][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 01:07:45.576][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 01:07:45.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 01:07:45.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 01:07:45.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 01:07:45.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 01:07:45.584][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-04 01:07:45.584][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-04 01:07:45.586][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 01:07:45.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 01:07:45.588][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 01:07:45.589][self$setPropertyValue]
biodb.DEBUG[2024-05-04 01:07:45.591][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-04 01:07:45.592][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 01:07:45.596][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:07:45.598][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-04 01:07:45.600][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-04 01:07:45.603][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-04 01:07:45.606][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-04 01:07:45.608][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-04 01:07:45.610][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-04 01:07:45.612][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-04 01:07:45.614][biodb::testThat]
biodb.INFO [2024-05-04 01:07:45.615][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-04 01:07:45.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 01:07:45.618][biodb::testThat]
biodb.DEBUG[2024-05-04 01:07:45.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-05-04 01:07:45.628][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 01:07:45.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-04 01:07:45.631][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 01:07:45.793][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-04 01:07:47.541][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-04 01:07:47.542][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 01:07:47.545][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-04 01:07:47.546][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-04 01:07:47.548][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 01:07:47.549][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 01:07:47.551][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-04 01:07:47.552][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 01:07:47.553][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 01:07:47.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:07:47.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:47.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:47.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:47.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:47.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:47.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:47.572][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-05-04 01:07:47.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:47.577][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 01:07:47.578][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:47.862][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:47.864][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:47.865][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:47.866][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:48.461][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:48.464][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:48.466][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:48.469][rule$waitAsNeeded] Wait 0.110152 second(s).
biodb.TRACE[2024-05-04 01:07:48.584][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:48.868][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:48.870][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:48.871][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:48.873][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:49.463][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:49.465][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:49.466][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:49.467][rule$waitAsNeeded] Wait 0.116394 second(s).
biodb.TRACE[2024-05-04 01:07:49.588][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:49.876][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:49.877][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:49.879][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:49.881][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:50.468][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:50.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:50.472][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:50.475][rule$waitAsNeeded] Wait 0.113011 second(s).
biodb.TRACE[2024-05-04 01:07:50.591][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:50.881][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:50.883][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:50.885][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:50.887][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:51.484][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:51.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:51.488][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:51.491][rule$waitAsNeeded] Wait 0.099937 second(s).
biodb.TRACE[2024-05-04 01:07:51.607][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:51.891][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:51.893][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:51.894][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:51.896][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:52.483][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:52.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:52.486][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:52.488][rule$waitAsNeeded] Wait 0.118389 second(s).
biodb.TRACE[2024-05-04 01:07:52.623][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:52.911][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:52.913][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:52.914][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:52.916][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:53.499][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:53.501][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:53.502][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:53.504][rule$waitAsNeeded] Wait 0.118704 second(s).
biodb.TRACE[2024-05-04 01:07:53.639][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:53.925][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:53.926][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:53.927][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:53.929][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:54.516][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:54.518][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:54.519][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:54.521][rule$waitAsNeeded] Wait 0.117829 second(s).
biodb.TRACE[2024-05-04 01:07:54.655][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:54.944][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:54.945][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:54.947][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:54.950][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:55.533][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:55.535][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:55.538][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:55.540][rule$waitAsNeeded] Wait 0.115128 second(s).
biodb.TRACE[2024-05-04 01:07:55.672][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:55.963][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:55.964][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:55.966][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:55.967][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:56.564][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:56.567][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:56.569][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:56.571][rule$waitAsNeeded] Wait 0.0997941 second(s).
biodb.TRACE[2024-05-04 01:07:56.687][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-05-04 01:07:56.975][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:56.976][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:56.977][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:56.979][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-05-04 01:07:57.565][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:57.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:07:57.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:07:57.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:07:57.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:07:57.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:07:57.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:07:57.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 01:07:57.593][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-05-04 01:07:57.598][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:57.600][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:57.602][rule$waitAsNeeded] Wait 0.084944 second(s).
biodb.TRACE[2024-05-04 01:07:57.704][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:07:57.999][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:58.001][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:58.003][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[2024-05-04 01:07:58.006][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:07:58.597][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:07:58.600][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:58.603][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:58.606][rule$waitAsNeeded] Wait 0.0978961 second(s).
biodb.TRACE[2024-05-04 01:07:58.720][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:07:59.015][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:07:59.017][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:07:59.018][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:07:59.020][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:07:59.613][private$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[2024-05-04 01:07:59.615][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:07:59.617][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:07:59.620][rule$waitAsNeeded] Wait 0.0996139 second(s).
biodb.TRACE[2024-05-04 01:07:59.736][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:00.032][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:00.034][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:00.036][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[2024-05-04 01:08:00.039][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:00.628][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:08:00.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:08:00.632][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:08:00.633][rule$waitAsNeeded] Wait 0.101971 second(s).
biodb.TRACE[2024-05-04 01:08:00.752][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:01.041][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:01.043][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:01.045][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:08:01.046][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:01.633][private$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[2024-05-04 01:08:01.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:08:01.637][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:08:01.640][rule$waitAsNeeded] Wait 0.112122 second(s).
biodb.TRACE[2024-05-04 01:08:01.757][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:02.049][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:02.052][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:02.054][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[2024-05-04 01:08:02.056][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:02.653][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:08:02.655][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:08:02.657][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:08:02.660][rule$waitAsNeeded] Wait 0.0966408 second(s).
biodb.TRACE[2024-05-04 01:08:02.760][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:03.045][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:03.047][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:03.048][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:08:03.052][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:03.637][private$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[2024-05-04 01:08:03.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:08:03.642][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:08:03.644][rule$waitAsNeeded] Wait 0.115433 second(s).
biodb.TRACE[2024-05-04 01:08:03.776][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:04.061][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:04.063][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:04.064][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[2024-05-04 01:08:04.066][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:04.653][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:08:04.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:08:04.655][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:08:04.657][rule$waitAsNeeded] Wait 0.118553 second(s).
biodb.TRACE[2024-05-04 01:08:04.792][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:05.084][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:05.085][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:05.087][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:08:05.088][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:05.670][private$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[2024-05-04 01:08:05.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:08:05.674][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:08:05.676][rule$waitAsNeeded] Wait 0.115833 second(s).
biodb.TRACE[2024-05-04 01:08:05.809][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:06.093][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:06.095][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:06.096][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[2024-05-04 01:08:06.097][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:06.686][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-05-04 01:08:06.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 01:08:06.691][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-05-04 01:08:06.693][rule$waitAsNeeded] Wait 0.115193 second(s).
biodb.TRACE[2024-05-04 01:08:06.824][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-05-04 01:08:07.106][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-05-04 01:08:07.108][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 01:08:07.109][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 01:08:07.111][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-05-04 01:08:07.701][private$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[2024-05-04 01:08:07.705][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2024-05-04 01:08:07.709][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 01:08:07.710][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-04 01:08:07.712][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-04 01:08:07.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:08:07.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:08:07.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:08:07.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:08:07.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:08:07.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:08:07.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:08:07.761][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.769][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:08:07.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:08:07.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:08:07.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:08:07.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:08:07.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:08:07.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:08:07.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:08:07.829][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.836][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-04 01:08:07.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 01:08:07.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 01:08:07.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 01:08:07.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 01:08:07.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 01:08:07.908][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-04 01:08:07.909][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 01:08:07.912][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 01:08:07.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:08:07.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:08:07.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:08:07.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:08:07.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:08:07.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:08:07.946][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.TRACE[2024-05-04 01:08:07.949][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-05-04 01:08:07.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 01:08:07.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:08:07.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:08:07.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:08:07.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:08:07.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:08:07.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 01:08:07.970][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-05-04 01:08:07.972][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 01:08:07.974][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-04 01:08:07.991][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 01:08:07.993][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-04 01:08:07.994][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-04 01:08:07.995][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 01:08:07.997][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 01:08:07.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 01:08:07.999][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 01:08:08.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 01:08:08.001][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 01:08:08.002][FUN] Functions in observer 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 3.36 2.2560.71
LipidmapsStructureEntry0.690.010.70