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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

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

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-12 21:01:51 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 21:06:54 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 302.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


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

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-06-12 21:02:37.662][biodb::testContext]
biodb.INFO [2024-06-12 21:02:37.665][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-12 21:02:37.666][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-12 21:02:37.667][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-12 21:02:37.668][biodb::testContext]
biodb.INFO [2024-06-12 21:02:37.675][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-12 21:02:37.677][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-12 21:02:37.685][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:02:37.686][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-12 21:02:37.687][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-12 21:02:37.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.691][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-12 21:02:37.711][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-12 21:02:37.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.715][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-12 21:02:37.716][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-12 21:02:37.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.720][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-12 21:02:37.721][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-12 21:02:37.722][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-12 21:02:37.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.725][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-12 21:02:37.726][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-12 21:02:37.728][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-12 21:02:37.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.731][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-12 21:02:37.732][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-12 21:02:37.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.736][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-12 21:02:37.737][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-12 21:02:37.738][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-12 21:02:37.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.742][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-12 21:02:37.743][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-12 21:02:37.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.747][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-12 21:02:37.748][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-12 21:02:37.749][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-12 21:02:37.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.753][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-12 21:02:37.754][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-12 21:02:37.755][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-12 21:02:37.756][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-12 21:02:37.757][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-12 21:02:37.758][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-12 21:02:37.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.762][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-12 21:02:37.763][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-12 21:02:37.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.766][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-12 21:02:37.767][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-12 21:02:37.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.771][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-12 21:02:37.772][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-12 21:02:37.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.776][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-12 21:02:37.777][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-12 21:02:37.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.781][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-12 21:02:37.782][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-12 21:02:37.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.785][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-12 21:02:37.787][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-12 21:02:37.792][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-12 21:02:37.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.795][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-12 21:02:37.796][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-12 21:02:37.797][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-12 21:02:37.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.804][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-12 21:02:37.840][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.864][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-12 21:02:37.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.866][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:02:37.867][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.870][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.871][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:02:37.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:02:37.873][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.874][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-12 21:02:37.875][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:02:37.876][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.877][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.877][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:02:37.877][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:02:37.877][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-12 21:02:37.877][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-12 21:02:37.877][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-12 21:02:37.878][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:02:37.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:02:37.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.884][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.884][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:02:37.886][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:02:37.887][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.888][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.889][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-12 21:02:37.891][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.892][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-12 21:02:37.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.894][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:02:37.895][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.895][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.896][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.897][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.898][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-12 21:02:37.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:02:37.900][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.901][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-12 21:02:37.902][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:02:37.903][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.904][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.905][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:02:37.905][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:02:37.905][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-12 21:02:37.905][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-12 21:02:37.905][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-12 21:02:37.906][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:02:37.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.913][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:02:37.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.916][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.917][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.918][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:02:37.919][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:02:37.920][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.921][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.922][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-12 21:02:37.924][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.925][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-12 21:02:37.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:02:37.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.930][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.931][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.932][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:02:37.933][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:02:37.934][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.935][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-12 21:02:37.936][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:02:37.937][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.938][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.939][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.940][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:02:37.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.943][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:02:37.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.946][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.947][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.948][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:02:37.949][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:02:37.950][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.951][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.952][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-12 21:02:37.954][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.955][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-12 21:02:37.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:02:37.958][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.959][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.961][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.962][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-12 21:02:37.963][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:02:37.964][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.965][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-12 21:02:37.966][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:02:37.967][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.968][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:37.969][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:02:37.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:02:37.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:37.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:37.976][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:02:37.977][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.978][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:02:37.979][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:02:37.980][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:37.981][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:37.985][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:02:37.986][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:37.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:37.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.992][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[2024-06-12 21:02:37.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:37.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:37.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:37.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:37.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:37.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:37.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.065][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-12 21:02:38.071][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-12 21:02:38.072][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-12 21:02:38.074][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-12 21:02:38.075][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-12 21:02:38.077][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-12 21:02:38.078][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-12 21:02:38.079][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-12 21:02:38.081][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-12 21:02:38.082][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-12 21:02:38.083][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-12 21:02:38.085][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-12 21:02:38.086][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-12 21:02:38.088][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-12 21:02:38.089][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-12 21:02:38.090][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-12 21:02:38.092][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-12 21:02:38.093][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-12 21:02:38.095][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-12 21:02:38.096][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-12 21:02:38.097][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-12 21:02:38.099][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-12 21:02:38.100][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-12 21:02:38.101][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-12 21:02:38.103][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-12 21:02:38.104][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-12 21:02:38.106][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-12 21:02:38.107][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-12 21:02:38.108][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-12 21:02:38.110][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-12 21:02:38.111][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-12 21:02:38.113][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-12 21:02:38.114][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-12 21:02:38.115][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-12 21:02:38.117][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-12 21:02:38.118][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-12 21:02:38.120][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-12 21:02:38.133][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-12 21:02:38.135][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-12 21:02:38.136][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-12 21:02:38.138][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-12 21:02:38.139][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-12 21:02:38.141][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-12 21:02:38.142][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-12 21:02:38.144][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-12 21:02:38.145][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-12 21:02:38.147][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-12 21:02:38.148][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-12 21:02:38.149][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-12 21:02:38.151][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-12 21:02:38.152][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-12 21:02:38.154][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-12 21:02:38.155][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-12 21:02:38.157][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-12 21:02:38.158][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-12 21:02:38.159][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-12 21:02:38.161][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-12 21:02:38.162][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-12 21:02:38.164][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-12 21:02:38.165][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-12 21:02:38.167][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-12 21:02:38.168][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-12 21:02:38.169][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-12 21:02:38.171][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-12 21:02:38.172][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-12 21:02:38.174][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-12 21:02:38.175][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-12 21:02:38.176][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-12 21:02:38.178][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-12 21:02:38.179][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-12 21:02:38.180][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-12 21:02:38.182][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-12 21:02:38.183][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-12 21:02:38.185][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-12 21:02:38.186][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-12 21:02:38.187][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-12 21:02:38.188][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-12 21:02:38.190][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-12 21:02:38.191][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-12 21:02:38.192][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-12 21:02:38.194][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-12 21:02:38.195][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-12 21:02:38.196][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-12 21:02:38.202][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-12 21:02:38.204][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-12 21:02:38.207][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:02:38.208][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.209][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.237][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[2024-06-12 21:02:38.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:02:38.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:02:38.315][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-12 21:02:38.324][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:02:38.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:38.327][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-12 21:02:38.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:38.329][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:02:38.329][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:38.330][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:02:38.331][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:38.332][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:02:38.333][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:02:38.334][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:02:38.335][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:38.336][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-12 21:02:38.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-12 21:02:38.338][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-12 21:02:38.339][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-12 21:02:38.340][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:02:38.340][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:02:38.341][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:02:38.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:38.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:38.343][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:02:38.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:02:38.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:02:38.346][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:02:38.347][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-12 21:02:38.347][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-12 21:02:38.348][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:02:38.349][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:02:38.350][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-12 21:02:38.351][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:02:38.356][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-12 21:02:38.358][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-12 21:02:38.387][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:02:38.388][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-12 21:02:38.393][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:02:38.397][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-12 21:02:38.401][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-12 21:02:38.402][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-12 21:02:38.404][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-12 21:02:38.405][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-12 21:02:38.414][biodb::testThat]
biodb.INFO [2024-06-12 21:02:38.415][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-12 21:02:38.416][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:38.417][biodb::testThat]
biodb.TRACE[2024-06-12 21:02:38.421][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-12 21:02:38.423][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-12 21:02:38.426][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-12 21:02:38.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:02:38.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:38.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:38.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:38.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:38.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:38.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:02:38.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:02:38.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:02:38.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.495][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:02:38.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:02:38.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.499][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:02:38.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:02:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.504][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:38.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:38.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.534][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:38.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:38.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:02:38.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.552][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:02:38.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:38.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:38.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.560][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:38.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:38.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.574][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:02:38.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.578][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-12 21:02:38.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.590][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:02:38.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.686][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.690][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:02:38.726][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-12 21:02:38.729][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:02:38.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:02:38.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.733][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:02:38.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:02:38.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.737][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-12 21:02:38.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-12 21:02:38.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.741][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-12 21:02:38.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-12 21:02:38.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.780][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.819][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.823][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:38.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.847][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.848][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.850][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:38.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:38.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.876][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.877][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:38.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:38.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.892][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.942][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.943][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.945][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:38.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:38.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:38.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.962][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:38.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:38.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.966][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:38.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:38.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.970][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:38.971][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:38.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:38.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:38.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:38.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:38.997][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.998][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:38.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.000][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:39.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:39.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.013][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.017][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.021][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.025][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.026][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.028][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.029][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.040][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.041][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.043][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.048][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:39.049][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:39.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.055][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:39.056][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:39.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.062][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:39.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:39.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.065][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.070][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.071][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.073][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.077][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.078][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.080][ef$get] fields variable is a list.
biodb.INFO [2024-06-12 21:02:39.088][biodb::testThat]
biodb.INFO [2024-06-12 21:02:39.089][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-12 21:02:39.090][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:39.091][biodb::testThat]
biodb.DEBUG[2024-06-12 21:02:39.105][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-12 21:02:39.113][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-12 21:02:39.118][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-12 21:02:39.120][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-12 21:02:39.121][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-12 21:02:39.122][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-12 21:02:39.146][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-12 21:02:39.148][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-12 21:02:39.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:02:39.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:02:39.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:02:39.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:02:39.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:02:39.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:02:39.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:02:39.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:02:39.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:02:39.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:02:39.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:02:39.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.187][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:02:39.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:02:39.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.191][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:02:39.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:02:39.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.199][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:02:39.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.203][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:39.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:39.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.208][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:39.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:02:39.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.212][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:02:39.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:39.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.216][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:02:39.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:39.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:39.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:39.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.224][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:02:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:02:39.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.236][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:02:39.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.240][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-12 21:02:39.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.253][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:02:39.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:39.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:39.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.280][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:39.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:39.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.288][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:39.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:02:39.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:02:39.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:02:39.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:02:39.316][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-12 21:02:39.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-12 21:02:39.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-12 21:02:39.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-12 21:02:39.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-12 21:02:39.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-12 21:02:39.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-12 21:02:39.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-12 21:02:39.336][biodb::testThat]
biodb.INFO [2024-06-12 21:02:39.337][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-12 21:02:39.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:39.339][biodb::testThat]
biodb.TRACE[2024-06-12 21:02:39.342][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.345][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:02:39.346][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-12 21:02:39.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:39.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:39.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:39.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:02:39.391][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-12 21:02:39.396][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-12 21:02:39.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:02:39.421][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:02:39.422][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-12 21:02:40.438][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-12 21:02:41.390][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:02:41.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-12 21:02:41.410][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-12 21:02:41.413][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-12 21:02:41.426][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:41.428][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:41.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.430][ef$get] fields variable is a list.
biodb.INFO [2024-06-12 21:02:41.434][biodb::testThat]
biodb.INFO [2024-06-12 21:02:41.435][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-12 21:02:41.436][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:41.437][biodb::testThat]
biodb.TRACE[2024-06-12 21:02:41.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:41.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:41.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:41.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:41.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:41.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:41.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:02:41.593][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-12 21:02:41.596][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-12 21:02:41.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-12 21:02:41.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-12 21:02:41.624][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-12 21:02:41.664][biodb::testThat]
biodb.INFO [2024-06-12 21:02:41.665][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-12 21:02:41.666][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:41.667][biodb::testThat]
biodb.TRACE[2024-06-12 21:02:41.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.693][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.697][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-12 21:02:41.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-12 21:02:41.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.701][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-12 21:02:41.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-12 21:02:41.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.750][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:02:41.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.759][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-12 21:02:41.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-12 21:02:41.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:41.763][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-12 21:02:41.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-12 21:02:41.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:41.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-12 21:02:41.772][biodb::testThat]
biodb.INFO [2024-06-12 21:02:41.773][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-12 21:02:41.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:41.775][biodb::testThat]
biodb.INFO [2024-06-12 21:02:41.783][biodb::testThat]
biodb.INFO [2024-06-12 21:02:41.784][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-12 21:02:41.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:41.785][biodb::testThat]
biodb.INFO [2024-06-12 21:02:41.792][biodb::testThat]
biodb.INFO [2024-06-12 21:02:41.793][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-12 21:02:41.794][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:41.795][biodb::testThat]
biodb.DEBUG[2024-06-12 21:02:41.799][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-12 21:02:42.572][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-12 21:02:43.042][biodb::testThat]
biodb.INFO [2024-06-12 21:02:43.044][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-12 21:02:43.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:43.046][biodb::testThat]
biodb.TRACE[2024-06-12 21:02:43.052][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:43.053][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:43.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.055][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.056][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.057][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.058][ef$get] fields variable is a list.
biodb.INFO [2024-06-12 21:02:43.060][biodb::testThat]
biodb.INFO [2024-06-12 21:02:43.061][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-12 21:02:43.062][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:02:43.063][biodb::testThat]
biodb.TRACE[2024-06-12 21:02:43.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:43.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:43.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:43.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:43.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:02:43.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:02:43.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:02:43.172][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-12 21:02:43.176][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-12 21:02:43.177][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-12 21:02:43.179][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-12 21:02:43.180][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-12 21:02:43.238][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-12 21:02:43.241][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-12 21:02:43.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-12 21:02:43.244][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-12 21:02:43.245][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-12 21:02:43.257][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-12 21:02:43.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-12 21:02:43.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-12 21:02:43.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-12 21:02:43.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:02:43.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:02:43.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:02:43.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:02:43.305][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-12 21:02:43.321][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:02:43.322][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:02:43.337][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-12 21:02:47.420][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-12 21:02:57.396][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:02:57.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-12 21:02:57.410][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-12 21:02:58.405][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-12 21:02:58.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:02:58.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:02:58.412][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-12 21:02:59.074][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-12 21:02:59.723][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:02:59.725][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-12 21:02:59.729][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-12 21:02:59.747][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-12 21:02:59.751][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:02:59.752][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:02:59.754][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-06-12 21:03:00.390][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-06-12 21:03:01.029][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:03:01.031][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-12 21:03:01.035][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-12 21:03:01.050][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:01.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:01.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:01.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-12 21:03:01.061][biodb::testThat]
biodb.INFO [2024-06-12 21:03:01.062][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-12 21:03:01.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:03:01.064][biodb::testThat]
biodb.TRACE[2024-06-12 21:03:01.067][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-12 21:03:01.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-12 21:03:01.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:01.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:01.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-12 21:03:01.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-12 21:03:01.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:01.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:01.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:01.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:01.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:01.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:01.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:01.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:01.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:01.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:01.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:03:01.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:01.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:01.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:01.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:01.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:01.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:01.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:03:01.107][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-12 21:03:01.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:01.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:01.113][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-12 21:03:05.042][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-12 21:03:15.195][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:03:15.201][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-12 21:03:15.221][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-12 21:03:16.493][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-12 21:03:16.544][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-12 21:03:16.546][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-12 21:03:16.547][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-12 21:03:16.549][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-12 21:03:16.550][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-12 21:03:16.551][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-12 21:03:16.552][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-12 21:03:16.553][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-12 21:03:16.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:16.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:16.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:16.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:16.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:16.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:16.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:03:16.580][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-12 21:03:16.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:16.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:16.585][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-12 21:03:17.238][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-06-12 21:03:17.907][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:03:17.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-06-12 21:03:17.917][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-06-12 21:03:17.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:17.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:17.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:17.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:17.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:17.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:17.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:03:17.938][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-12 21:03:17.943][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:17.945][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:17.949][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-12 21:03:18.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-12 21:03:19.261][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:03:19.267][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-12 21:03:19.273][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-12 21:03:19.278][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-12 21:03:19.281][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-12 21:03:19.284][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-12 21:03:19.286][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-12 21:03:19.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:19.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:19.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:19.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:19.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:19.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:19.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:19.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:03:19.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:03:19.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:03:19.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:03:19.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.409][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:03:19.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:03:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.417][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:03:19.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:03:19.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.424][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.432][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.448][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:03:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.453][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:03:19.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:19.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:03:19.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:03:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:03:19.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:03:19.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:03:19.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.498][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-12 21:03:19.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:03:19.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.525][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.533][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:03:19.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:19.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:19.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:19.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:19.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:19.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:19.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:19.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:03:19.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:03:19.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.658][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:03:19.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:03:19.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.666][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:03:19.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:03:19.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.673][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.682][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:03:19.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.689][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.697][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:03:19.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.705][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:03:19.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:19.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.713][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:03:19.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:19.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:03:19.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:03:19.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:03:19.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:03:19.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.741][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:03:19.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.747][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-12 21:03:19.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:03:19.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.768][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:03:19.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:03:19.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.775][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.780][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.789][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:19.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:19.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:03:19.835][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-12 21:03:19.847][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-12 21:03:19.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:19.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:19.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:19.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:19.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:19.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:19.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:19.883][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.892][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.899][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:19.901][private$selectFields]
biodb.TRACE[2024-06-12 21:03:19.903][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:19.904][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:19.906][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:19.908][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.910][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.913][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.914][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.916][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.920][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:19.921][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:19.923][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.924][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.927][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.928][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:19.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.938][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.960][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-12 21:03:19.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:19.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:19.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:19.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:19.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:19.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:19.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.983][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:19.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:19.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:19.991][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:19.992][private$selectFields]
biodb.TRACE[2024-06-12 21:03:19.994][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:19.995][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:19.996][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:19.998][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.000][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.004][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.005][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.008][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:20.009][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:20.010][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.012][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.013][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.015][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:20.016][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.022][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.032][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-12 21:03:20.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:20.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:20.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:20.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:20.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:20.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:20.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.047][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.053][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:20.053][private$selectFields]
biodb.TRACE[2024-06-12 21:03:20.055][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:20.056][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:20.057][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:20.059][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.061][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.066][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.067][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.071][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.072][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:20.073][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:20.075][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.077][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.080][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.082][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:20.116][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.125][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.139][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-12 21:03:20.140][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-12 21:03:20.141][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-12 21:03:20.151][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:20.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:20.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-12 21:03:20.158][biodb::testThat]
biodb.INFO [2024-06-12 21:03:20.159][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-12 21:03:20.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:03:20.161][biodb::testThat]
biodb.TRACE[2024-06-12 21:03:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-12 21:03:20.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-12 21:03:20.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-12 21:03:20.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-12 21:03:20.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:20.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:20.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:20.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:03:20.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:20.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:20.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:20.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:20.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:20.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:20.259][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[2024-06-12 21:03:20.264][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-06-12 21:03:20.271][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:20.274][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:20.301][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-06-12 21:03:24.712][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-06-12 21:03:34.872][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:03:34.878][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-12 21:03:34.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-12 21:03:36.815][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-12 21:03:36.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:36.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:36.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:36.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:36.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:36.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:36.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:36.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:36.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:36.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:36.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:36.940][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:36.941][private$selectFields]
biodb.TRACE[2024-06-12 21:03:36.943][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:36.945][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:36.946][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:36.948][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.950][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:36.953][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:36.955][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.956][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:36.959][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:36.961][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:36.979][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:36.981][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.984][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:36.988][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:36.989][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:36.991][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:36.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:36.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:36.999][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.005][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.013][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-12 21:03:37.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:37.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:37.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:37.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:37.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:37.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:37.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:37.034][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.041][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.048][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.049][private$selectFields]
biodb.TRACE[2024-06-12 21:03:37.051][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:37.053][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:37.054][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.056][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.058][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.061][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.063][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.065][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.068][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.070][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.071][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.073][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.075][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.078][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.079][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:37.081][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.088][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.102][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-12 21:03:37.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:37.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:37.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:37.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:37.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:37.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:37.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:37.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.143][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.145][private$selectFields]
biodb.TRACE[2024-06-12 21:03:37.147][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:37.149][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:37.152][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.154][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.156][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.161][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.163][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.166][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.170][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.172][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.175][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:37.177][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.179][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.184][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.186][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:37.189][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.196][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.203][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.210][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-12 21:03:37.211][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-12 21:03:37.213][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-12 21:03:37.229][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:37.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:37.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-12 21:03:37.242][biodb::testThat]
biodb.INFO [2024-06-12 21:03:37.244][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-12 21:03:37.246][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:03:37.248][biodb::testThat]
biodb.TRACE[2024-06-12 21:03:37.254][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-12 21:03:37.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-12 21:03:37.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-12 21:03:37.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-12 21:03:37.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:37.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:03:37.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:37.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:03:37.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:37.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:37.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:37.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:37.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:37.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:37.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:03:37.328][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-12 21:03:37.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-12 21:03:37.339][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-12 21:03:37.342][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-12 21:03:37.416][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-12 21:03:39.283][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-12 21:03:39.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:39.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:39.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:39.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:39.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:39.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:39.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:39.304][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.311][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.317][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.318][private$selectFields]
biodb.TRACE[2024-06-12 21:03:39.320][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:39.321][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:39.323][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.324][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.326][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.329][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.330][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.332][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.335][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.336][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.338][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.339][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.341][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.344][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.345][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:39.347][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.353][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.359][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.366][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-12 21:03:39.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:39.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:39.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:39.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:39.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:39.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:39.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:39.385][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.392][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.398][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.399][private$selectFields]
biodb.TRACE[2024-06-12 21:03:39.401][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:39.402][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:39.404][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.405][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.407][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.410][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.411][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.413][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.416][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.418][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.419][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.421][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.422][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.425][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.427][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:39.428][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.434][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.440][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.447][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-12 21:03:39.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:39.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:39.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:39.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:39.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:39.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:39.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:03:39.465][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.472][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.478][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.479][private$selectFields]
biodb.TRACE[2024-06-12 21:03:39.480][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-12 21:03:39.482][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:03:39.483][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.485][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.487][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.491][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.493][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.496][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.497][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.499][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:03:39.501][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.502][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.507][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-12 21:03:39.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.515][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.521][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:39.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:39.528][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-12 21:03:39.530][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-12 21:03:39.531][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-12 21:03:39.561][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:39.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-12 21:03:39.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:39.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-12 21:03:39.574][biodb::testThat]
biodb.INFO [2024-06-12 21:03:39.576][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-12 21:03:39.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:03:39.579][biodb::testThat]
biodb.DEBUG[2024-06-12 21:03:39.582][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-12 21:03:39.584][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-12 21:03:39.587][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-12 21:03:39.589][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-12 21:03:39.591][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-12 21:03:39.593][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-12 21:03:39.595][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-12 21:03:39.597][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-12 21:03:39.598][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-12 21:03:39.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:39.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:39.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:39.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:39.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:39.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:39.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:03:39.639][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-12 21:03:39.643][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:39.644][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:39.646][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:40.296][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:40.298][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:40.300][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:40.303][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:41.071][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:41.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:41.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:41.076][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:41.782][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:41.790][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:41.794][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:41.797][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:42.599][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:42.600][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:42.602][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:42.606][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:43.288][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:43.291][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:43.293][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:43.296][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:44.093][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:44.095][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:44.097][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:44.100][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:44.761][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:44.763][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:44.765][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:44.767][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:45.464][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:45.466][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:45.467][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:45.469][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:46.093][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:46.094][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:46.096][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:46.097][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:46.854][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:46.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:46.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:46.860][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:47.519][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:47.521][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:47.522][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:47.524][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:48.277][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:48.280][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:48.283][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:48.287][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:48.945][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:48.948][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:48.951][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:48.954][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:49.654][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:49.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:49.660][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:49.664][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:50.279][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:50.284][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:50.288][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:50.291][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:51.093][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:51.095][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:51.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:51.103][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:51.726][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:51.729][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:51.732][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:51.736][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:52.534][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:52.535][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:52.537][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:52.538][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-12 21:03:53.116][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:53.118][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:53.119][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:53.120][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-12 21:03:53.892][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-12 21:03:53.896][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-12 21:03:53.898][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-12 21:03:53.899][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-12 21:03:53.901][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-12 21:03:53.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:53.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:53.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:53.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:53.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:53.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:53.914][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.TRACE[2024-06-12 21:03:53.916][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:53.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:53.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:53.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:53.920][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:03:53.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:53.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:53.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:53.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:53.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:53.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:53.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:53.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:53.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:53.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:53.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:53.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:53.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:53.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:53.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:53.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:53.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:53.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:53.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:53.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:03:53.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:03:53.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:03:54.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:03:54.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:03:54.025][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-12 21:03:54.026][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-12 21:03:54.034][biodb::testThat]
biodb.INFO [2024-06-12 21:03:54.035][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-12 21:03:54.036][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:03:54.037][biodb::testThat]
biodb.DEBUG[2024-06-12 21:03:54.045][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-12 21:03:54.046][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-12 21:03:54.047][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-12 21:03:54.049][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-12 21:03:54.050][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-12 21:03:54.051][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-12 21:03:54.052][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-12 21:03:54.053][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-12 21:03:54.054][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-12 21:03:54.055][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-12 21:03:54.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:03:54.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:03:54.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:03:54.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:03:54.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:03:54.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:03:54.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:03:54.070][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-12 21:03:54.073][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:54.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:54.075][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:03:54.645][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:54.647][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:54.648][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:54.649][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:03:55.399][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:55.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:55.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:55.406][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:03:55.982][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:55.984][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:55.985][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:55.987][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:03:56.685][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:56.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:56.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:56.694][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:03:57.314][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:57.317][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:57.321][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:57.324][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:03:58.025][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:58.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:58.031][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:58.036][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:03:58.652][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:03:58.653][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:03:58.655][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:03:58.657][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:03:59.446][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:03:59.448][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:03:59.450][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:03:59.451][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:04:00.038][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:00.041][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:00.045][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:00.048][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:04:00.848][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:00.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:00.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:00.858][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:04:01.478][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:01.479][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:01.481][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:01.482][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:04:02.280][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:02.283][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:02.286][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:02.290][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:04:02.919][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:02.922][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:02.924][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:02.926][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:04:03.688][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:03.692][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:03.695][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:03.699][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:04:04.299][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:04.301][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:04.303][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:04.305][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:04:05.084][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:05.086][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:05.088][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:05.091][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:04:05.688][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:05.690][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:05.692][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:05.694][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:04:06.466][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:06.469][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:06.471][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:06.475][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-12 21:04:07.103][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:07.107][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:07.110][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:07.113][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-12 21:04:07.878][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:07.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:04:07.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:07.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:07.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:07.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:07.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:07.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:07.928][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-12 21:04:07.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:07.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:07.940][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:08.533][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:08.535][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:08.538][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:08.541][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:09.337][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:09.338][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:09.340][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:09.341][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:09.911][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:09.913][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:09.915][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:09.916][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:10.613][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:10.614][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:10.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:10.617][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:11.196][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:11.198][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:11.201][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:11.204][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:11.971][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:11.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:11.976][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:11.980][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:12.549][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:12.550][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:12.552][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:12.553][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:13.248][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:13.249][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:13.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:13.252][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:13.831][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:13.832][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:13.834][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:13.835][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:14.585][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:14.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:14.588][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:14.589][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:15.171][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:15.173][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:15.175][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:15.177][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:15.958][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:15.959][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:15.961][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:15.962][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:16.543][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:16.544][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:16.546][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:16.547][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:17.297][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:17.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:17.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:17.302][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:17.878][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:17.880][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:17.881][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:17.882][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:18.634][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:18.636][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:18.637][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:18.639][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:19.213][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:19.214][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:19.215][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:19.217][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:19.912][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-12 21:04:19.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:19.916][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:19.918][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-12 21:04:20.486][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-12 21:04:20.487][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-12 21:04:20.488][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-12 21:04:20.490][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-12 21:04:21.244][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-12 21:04:21.249][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-12 21:04:21.252][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-12 21:04:21.254][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-12 21:04:21.256][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-12 21:04:21.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:04:21.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:21.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:21.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:21.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:21.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:21.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:04:21.277][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.283][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:04:21.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:04:21.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:21.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:21.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:21.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:21.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:21.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:04:21.306][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.310][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:21.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:21.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:21.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:21.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:21.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:04:21.368][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-12 21:04:21.369][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-12 21:04:21.371][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-12 21:04:21.656][biodb::testThat]
biodb.INFO [2024-06-12 21:04:21.657][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-12 21:04:21.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:21.659][biodb::testThat]
biodb.INFO [2024-06-12 21:04:21.709][biodb::testThat]
biodb.INFO [2024-06-12 21:04:21.710][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-12 21:04:21.712][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:21.713][biodb::testThat]
biodb.INFO [2024-06-12 21:04:21.721][biodb::testThat]
biodb.INFO [2024-06-12 21:04:21.722][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-12 21:04:21.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:21.724][biodb::testThat]
biodb.DEBUG[2024-06-12 21:04:21.727][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-12 21:04:21.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:21.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:21.734][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-12 21:04:25.729][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-12 21:04:35.558][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:04:35.561][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-12 21:04:35.573][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-12 21:04:36.716][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:36.718][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:36.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:36.720][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:36.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:36.722][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:36.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:36.724][ef$get] fields variable is a list.
biodb.INFO [2024-06-12 21:04:36.726][biodb::testThat]
biodb.INFO [2024-06-12 21:04:36.727][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-12 21:04:36.728][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:36.729][biodb::testThat]
biodb.ERROR[2024-06-12 21:04:36.743][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-12 21:04:36.761][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-12 21:04:36.775][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-12 21:04:36.777][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-12 21:04:36.778][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-12 21:04:36.779][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-12 21:04:36.780][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:36.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:36.782][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:36.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:36.783][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-12 21:04:36.795][biodb::testContext]
biodb.INFO [2024-06-12 21:04:36.796][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-12 21:04:36.797][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-12 21:04:36.798][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-12 21:04:36.799][biodb::testContext]
biodb.INFO [2024-06-12 21:04:36.801][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-12 21:04:36.803][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-12 21:04:36.807][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:04:36.808][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-12 21:04:36.809][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-12 21:04:36.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.813][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-12 21:04:36.814][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-12 21:04:36.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.818][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-12 21:04:36.819][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-12 21:04:36.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.823][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-12 21:04:36.824][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-12 21:04:36.825][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-12 21:04:36.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.828][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-12 21:04:36.829][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-12 21:04:36.830][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-12 21:04:36.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.834][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-12 21:04:36.835][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-12 21:04:36.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.839][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-12 21:04:36.840][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-12 21:04:36.841][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-12 21:04:36.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.845][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-12 21:04:36.846][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-12 21:04:36.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.849][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-12 21:04:36.850][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-12 21:04:36.851][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-12 21:04:36.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.855][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-12 21:04:36.856][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-12 21:04:36.857][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-12 21:04:36.858][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-12 21:04:36.859][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-12 21:04:36.860][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-12 21:04:36.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.864][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-12 21:04:36.865][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-12 21:04:36.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.869][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-12 21:04:36.870][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-12 21:04:36.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.874][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-12 21:04:36.875][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-12 21:04:36.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.879][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-12 21:04:36.880][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-12 21:04:36.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.886][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-12 21:04:36.887][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-12 21:04:36.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.891][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-12 21:04:36.892][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-12 21:04:36.895][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-12 21:04:36.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:36.899][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-12 21:04:36.900][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-12 21:04:36.901][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-12 21:04:36.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:36.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:36.904][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[2024-06-12 21:04:36.905][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-12 21:04:36.907][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.908][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-12 21:04:36.909][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.910][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:36.911][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.912][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.913][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.914][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.915][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:04:36.916][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:36.917][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.918][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-12 21:04:36.919][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:36.920][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.922][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:04:36.922][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:04:36.922][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-12 21:04:36.922][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-12 21:04:36.922][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-12 21:04:36.924][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:36.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:36.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:36.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:36.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:36.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:36.929][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.930][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.932][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:36.932][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:36.933][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.934][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.936][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-12 21:04:36.937][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.939][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-12 21:04:36.940][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.941][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:36.942][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.943][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.944][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.946][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-12 21:04:36.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:36.948][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.949][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-12 21:04:36.950][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:36.951][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.952][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.953][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:04:36.953][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:04:36.953][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-12 21:04:36.953][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-12 21:04:36.953][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-12 21:04:36.954][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:36.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:36.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:36.957][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:36.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:36.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:36.960][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.961][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:36.963][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:36.964][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.965][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.966][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-12 21:04:36.968][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.969][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-12 21:04:36.970][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.971][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:36.972][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.974][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.975][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.976][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:04:36.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:36.978][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.979][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-12 21:04:36.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:36.981][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.982][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:36.983][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.985][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:36.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:36.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:36.988][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:36.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:36.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:36.991][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:36.992][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.993][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:36.994][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:36.995][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:36.996][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:36.997][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-12 21:04:36.999][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.000][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-12 21:04:37.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:37.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:37.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:37.006][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:37.007][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-12 21:04:37.008][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:37.009][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:37.010][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-12 21:04:37.011][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:37.012][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:37.013][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.014][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:37.015][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:37.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:37.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:37.018][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:37.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:37.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:37.022][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:37.023][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:37.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:37.025][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:37.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:37.027][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:37.028][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:04:37.029][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.040][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.DEBUG[2024-06-12 21:04:37.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.133][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[2024-06-12 21:04:37.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.147][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-12 21:04:37.148][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-12 21:04:37.149][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-12 21:04:37.151][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-12 21:04:37.152][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-12 21:04:37.153][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-12 21:04:37.155][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-12 21:04:37.156][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-12 21:04:37.157][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-12 21:04:37.159][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-12 21:04:37.160][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-12 21:04:37.161][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-12 21:04:37.163][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-12 21:04:37.164][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-12 21:04:37.165][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-12 21:04:37.167][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-12 21:04:37.168][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-12 21:04:37.169][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-12 21:04:37.171][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-12 21:04:37.172][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-12 21:04:37.173][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-12 21:04:37.175][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-12 21:04:37.176][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-12 21:04:37.177][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-12 21:04:37.179][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-12 21:04:37.180][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-12 21:04:37.181][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-12 21:04:37.183][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-12 21:04:37.184][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-12 21:04:37.185][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-12 21:04:37.187][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-12 21:04:37.188][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-12 21:04:37.189][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-12 21:04:37.190][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-12 21:04:37.192][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-12 21:04:37.193][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-12 21:04:37.194][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-12 21:04:37.196][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-12 21:04:37.197][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-12 21:04:37.198][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-12 21:04:37.199][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-12 21:04:37.201][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-12 21:04:37.202][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-12 21:04:37.203][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-12 21:04:37.205][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-12 21:04:37.206][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-12 21:04:37.207][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-12 21:04:37.209][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-12 21:04:37.210][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-12 21:04:37.211][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-12 21:04:37.213][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-12 21:04:37.214][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-12 21:04:37.215][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-12 21:04:37.217][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-12 21:04:37.218][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-12 21:04:37.219][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-12 21:04:37.221][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-12 21:04:37.222][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-12 21:04:37.223][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-12 21:04:37.225][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-12 21:04:37.226][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-12 21:04:37.227][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-12 21:04:37.229][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-12 21:04:37.230][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-12 21:04:37.231][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-12 21:04:37.233][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-12 21:04:37.234][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-12 21:04:37.236][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-12 21:04:37.237][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-12 21:04:37.238][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-12 21:04:37.240][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-12 21:04:37.241][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-12 21:04:37.242][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-12 21:04:37.244][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-12 21:04:37.245][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-12 21:04:37.246][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-12 21:04:37.247][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-12 21:04:37.249][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-12 21:04:37.250][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-12 21:04:37.251][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-12 21:04:37.253][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-12 21:04:37.254][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-12 21:04:37.255][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-12 21:04:37.257][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-12 21:04:37.258][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-12 21:04:37.259][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:04:37.260][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.262][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:37.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:37.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:37.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:37.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:37.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:37.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:37.385][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-12 21:04:37.387][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:04:37.390][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:37.391][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-12 21:04:37.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:37.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:37.398][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.400][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:37.401][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:04:37.403][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:37.404][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.406][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-12 21:04:37.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-12 21:04:37.409][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-12 21:04:37.411][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:37.412][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:04:37.412][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:04:37.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:37.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:37.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:37.418][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:37.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:37.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:37.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:37.422][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-12 21:04:37.422][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-12 21:04:37.433][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:37.433][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:37.434][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:37.435][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:37.436][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-12 21:04:37.438][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-12 21:04:37.441][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:04:37.442][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-12 21:04:37.443][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:04:37.444][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-12 21:04:37.445][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-12 21:04:37.446][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-12 21:04:37.447][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-12 21:04:37.448][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-12 21:04:37.450][biodb::testThat]
biodb.INFO [2024-06-12 21:04:37.451][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-12 21:04:37.452][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:37.452][biodb::testThat]
biodb.DEBUG[2024-06-12 21:04:37.456][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-06-12 21:04:37.460][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:37.461][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:37.462][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-12 21:04:38.095][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-06-12 21:04:38.738][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:04:38.741][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-12 21:04:38.747][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-12 21:04:38.761][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-06-12 21:04:38.767][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:38.769][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:38.772][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-12 21:04:39.740][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-12 21:04:40.424][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:04:40.431][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-12 21:04:40.441][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-12 21:04:40.468][biodb::testThat]
biodb.INFO [2024-06-12 21:04:40.471][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-12 21:04:40.473][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:40.474][biodb::testThat]
biodb.INFO [2024-06-12 21:04:40.529][biodb::testThat]
biodb.INFO [2024-06-12 21:04:40.531][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-12 21:04:40.533][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:40.534][biodb::testThat]
biodb.DEBUG[2024-06-12 21:04:40.539][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-12 21:04:40.544][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:40.545][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:40.548][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-12 21:04:41.052][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-12 21:04:41.560][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:04:41.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-12 21:04:41.571][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-12 21:04:41.581][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-12 21:04:41.587][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-12 21:04:41.590][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-12 21:04:41.593][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-12 21:04:41.597][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-12 21:04:41.612][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-06-12 21:04:41.620][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:41.622][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:41.626][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-12 21:04:42.396][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-12 21:04:42.885][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:04:42.890][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-12 21:04:42.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-12 21:04:42.915][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-06-12 21:04:42.923][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:42.925][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:42.928][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-12 21:04:44.204][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-12 21:04:47.319][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:04:47.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-12 21:04:47.326][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-12 21:04:47.456][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-06-12 21:04:47.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-12 21:04:47.461][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-12 21:04:47.463][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-12 21:04:48.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-12 21:04:51.676][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-12 21:04:51.682][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-12 21:04:51.689][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-12 21:04:51.829][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-12 21:04:51.831][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-12 21:04:51.832][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-12 21:04:51.833][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-12 21:04:51.834][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:51.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:51.836][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:51.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:51.838][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-12 21:04:51.844][biodb::testContext]
biodb.INFO [2024-06-12 21:04:51.845][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-12 21:04:51.847][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-12 21:04:51.848][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-12 21:04:51.849][biodb::testContext]
biodb.INFO [2024-06-12 21:04:51.851][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-12 21:04:51.853][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-12 21:04:51.858][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:04:51.859][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-12 21:04:51.861][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-12 21:04:51.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.864][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[2024-06-12 21:04:51.865][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-12 21:04:51.866][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-12 21:04:51.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.870][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-12 21:04:51.871][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-12 21:04:51.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.875][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-12 21:04:51.877][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-12 21:04:51.878][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-12 21:04:51.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.882][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-12 21:04:51.883][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-12 21:04:51.884][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-12 21:04:51.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.889][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-12 21:04:51.890][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-12 21:04:51.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.894][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-12 21:04:51.895][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-12 21:04:51.896][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-12 21:04:51.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.899][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[2024-06-12 21:04:51.901][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-12 21:04:51.902][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-12 21:04:51.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.906][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-12 21:04:51.907][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-12 21:04:51.908][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-12 21:04:51.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.912][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-12 21:04:51.914][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-12 21:04:51.915][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-12 21:04:51.916][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-12 21:04:51.917][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-12 21:04:51.918][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-12 21:04:51.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.922][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-12 21:04:51.923][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-12 21:04:51.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.926][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[2024-06-12 21:04:51.927][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-12 21:04:51.929][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-12 21:04:51.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.933][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-12 21:04:51.934][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-12 21:04:51.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.938][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-12 21:04:51.939][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-12 21:04:51.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.944][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-12 21:04:51.945][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-12 21:04:51.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.949][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-12 21:04:51.950][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-12 21:04:51.955][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-12 21:04:51.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:51.960][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-12 21:04:51.961][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-12 21:04:51.962][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-12 21:04:51.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:51.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:51.965][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[2024-06-12 21:04:51.966][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-12 21:04:51.968][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:51.970][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-12 21:04:51.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:51.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:51.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:51.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.028][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.030][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:04:52.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:52.032][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.033][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-12 21:04:52.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:52.036][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.037][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.038][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:04:52.038][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:04:52.038][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-12 21:04:52.038][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-12 21:04:52.038][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-12 21:04:52.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:52.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.042][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:52.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.045][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.046][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.047][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:52.048][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:52.049][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.050][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.051][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-12 21:04:52.053][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.054][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-12 21:04:52.055][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.056][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:52.057][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.058][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.059][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.062][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-12 21:04:52.063][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:52.064][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.065][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-12 21:04:52.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:52.067][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.069][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:04:52.069][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:04:52.069][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-12 21:04:52.069][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-12 21:04:52.069][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-12 21:04:52.070][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:52.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:52.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.077][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:52.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:52.080][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.081][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.083][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-12 21:04:52.085][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.086][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-12 21:04:52.087][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.088][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:52.089][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.090][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.091][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.092][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.093][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:04:52.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:52.095][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.096][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-12 21:04:52.097][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:52.098][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.100][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.101][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.102][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:52.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:52.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.108][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.109][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:52.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:52.112][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.113][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.114][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-12 21:04:52.116][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.117][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-12 21:04:52.118][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.119][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:52.120][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.121][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.122][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.123][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.124][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-12 21:04:52.125][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:52.126][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.127][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-12 21:04:52.128][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:52.129][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.130][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.131][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.133][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:52.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:52.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.140][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.141][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:52.142][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:52.143][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.144][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.145][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:04:52.146][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.161][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[2024-06-12 21:04:52.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.166][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[2024-06-12 21:04:52.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.198][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[2024-06-12 21:04:52.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.223][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[2024-06-12 21:04:52.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.233][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-12 21:04:52.235][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-12 21:04:52.236][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-12 21:04:52.238][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-12 21:04:52.239][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-12 21:04:52.241][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-12 21:04:52.242][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-12 21:04:52.243][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-12 21:04:52.245][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-12 21:04:52.246][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-12 21:04:52.247][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-12 21:04:52.249][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-12 21:04:52.250][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-12 21:04:52.252][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-12 21:04:52.253][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-12 21:04:52.255][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-12 21:04:52.256][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-12 21:04:52.257][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-12 21:04:52.259][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-12 21:04:52.260][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-12 21:04:52.261][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-12 21:04:52.263][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-12 21:04:52.264][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-12 21:04:52.266][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-12 21:04:52.267][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-12 21:04:52.269][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-12 21:04:52.270][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-12 21:04:52.271][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-12 21:04:52.273][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-12 21:04:52.274][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-12 21:04:52.276][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-12 21:04:52.277][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-12 21:04:52.278][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-12 21:04:52.280][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-12 21:04:52.281][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-12 21:04:52.283][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-12 21:04:52.284][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-12 21:04:52.286][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-12 21:04:52.287][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-12 21:04:52.288][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-12 21:04:52.290][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-12 21:04:52.291][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-12 21:04:52.292][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-12 21:04:52.294][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-12 21:04:52.295][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-12 21:04:52.297][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-12 21:04:52.298][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-12 21:04:52.300][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-12 21:04:52.301][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-12 21:04:52.302][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-12 21:04:52.304][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-12 21:04:52.305][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-12 21:04:52.306][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-12 21:04:52.308][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-12 21:04:52.309][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-12 21:04:52.311][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-12 21:04:52.312][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-12 21:04:52.314][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-12 21:04:52.315][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-12 21:04:52.316][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-12 21:04:52.318][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-12 21:04:52.319][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-12 21:04:52.320][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-12 21:04:52.322][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-12 21:04:52.323][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-12 21:04:52.325][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-12 21:04:52.326][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-12 21:04:52.327][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-12 21:04:52.329][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-12 21:04:52.330][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-12 21:04:52.332][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-12 21:04:52.333][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-12 21:04:52.334][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-12 21:04:52.336][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-12 21:04:52.337][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-12 21:04:52.339][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-12 21:04:52.340][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-12 21:04:52.342][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-12 21:04:52.343][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-12 21:04:52.344][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-12 21:04:52.346][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-12 21:04:52.347][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-12 21:04:52.349][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-12 21:04:52.350][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-12 21:04:52.352][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-12 21:04:52.353][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-12 21:04:52.354][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.356][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.357][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.DEBUG[2024-06-12 21:04:52.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.432][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[2024-06-12 21:04:52.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.438][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[2024-06-12 21:04:52.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-12 21:04:52.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:52.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:52.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:52.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:52.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:52.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-12 21:04:52.475][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-12 21:04:52.477][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:04:52.478][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.479][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.480][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.481][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-12 21:04:52.482][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.483][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.484][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.485][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.486][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-12 21:04:52.487][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-12 21:04:52.488][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.489][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-12 21:04:52.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-12 21:04:52.491][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-12 21:04:52.492][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-12 21:04:52.493][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-12 21:04:52.493][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-12 21:04:52.494][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-12 21:04:52.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-12 21:04:52.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-12 21:04:52.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-12 21:04:52.499][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-12 21:04:52.500][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-12 21:04:52.500][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-12 21:04:52.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-12 21:04:52.502][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-12 21:04:52.503][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-12 21:04:52.504][self$setPropertyValue]
biodb.DEBUG[2024-06-12 21:04:52.505][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-12 21:04:52.506][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-12 21:04:52.510][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:04:52.511][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-12 21:04:52.512][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-12 21:04:52.513][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-12 21:04:52.514][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-12 21:04:52.515][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-12 21:04:52.517][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-12 21:04:52.518][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-12 21:04:52.519][biodb::testThat]
biodb.INFO [2024-06-12 21:04:52.520][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-12 21:04:52.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-12 21:04:52.522][biodb::testThat]
biodb.DEBUG[2024-06-12 21:04:52.526][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-12 21:04:52.530][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-12 21:04:52.531][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-12 21:04:52.532][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-12 21:04:52.581][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-12 21:04:53.499][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-12 21:04:53.500][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-12 21:04:53.503][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-12 21:04:53.504][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-12 21:04:53.506][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-12 21:04:53.507][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-12 21:04:53.508][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-12 21:04:53.510][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-12 21:04:53.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:04:53.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:53.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:53.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:53.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:53.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:53.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:04:53.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.544][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:04:53.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:04:53.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.548][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:04:53.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:04:53.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.553][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.557][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.570][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:04:53.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.574][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:04:53.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.579][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:53.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:53.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.583][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:53.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:53.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.596][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:04:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.600][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-12 21:04:53.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.613][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:04:53.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.643][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:04:53.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:04:53.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:53.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:53.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:53.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:53.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:53.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:04:53.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.703][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:04:53.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-12 21:04:53.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.707][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:04:53.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-12 21:04:53.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.712][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.730][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:04:53.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.734][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-12 21:04:53.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:53.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:53.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.743][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:53.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.756][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:04:53.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.760][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-12 21:04:53.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.773][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-12 21:04:53.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.777][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.790][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-12 21:04:53.832][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-06-12 21:04:53.835][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-12 21:04:53.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:04:53.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:53.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:53.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:53.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:53.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:53.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:04:53.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:04:53.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:04:53.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:04:53.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:04:53.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-12 21:04:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-12 21:04:53.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.876][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-12 21:04:53.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-12 21:04:53.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.880][private$selectFields] Fields none
biodb.TRACE[2024-06-12 21:04:53.881][private$selectFields]
biodb.TRACE[2024-06-12 21:04:53.882][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-12 21:04:53.883][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:04:53.884][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:04:53.885][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.886][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.888][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.888][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.889][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.892][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.893][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.895][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.896][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.897][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.900][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.901][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.903][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.904][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:53.905][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:53.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.907][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.908][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.910][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.911][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.912][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.914][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.915][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.916][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.919][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.920][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.922][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.923][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.925][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.926][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.927][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.929][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.930][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.931][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.933][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.934][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:53.935][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:53.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.937][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.940][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.941][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.942][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.944][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.945][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:04:53.946][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:04:53.947][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.948][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.951][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.952][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.953][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.954][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.955][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:53.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.957][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.958][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.959][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:53.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.961][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.962][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.963][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:53.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.966][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:53.967][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:53.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.969][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:53.970][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:53.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.972][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.973][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.974][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:53.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.976][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.977][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-12 21:04:53.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:53.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:53.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:53.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:53.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:53.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.002][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.009][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.013][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.017][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.021][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.060][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.067][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.077][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-06-12 21:04:54.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-12 21:04:54.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:54.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:54.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:54.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:54.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:54.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-12 21:04:54.089][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:04:54.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:04:54.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.093][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-12 21:04:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-12 21:04:54.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.097][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-12 21:04:54.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-12 21:04:54.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-12 21:04:54.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-12 21:04:54.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.104][private$selectFields] Fields none
biodb.TRACE[2024-06-12 21:04:54.105][private$selectFields]
biodb.TRACE[2024-06-12 21:04:54.106][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-12 21:04:54.107][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-12 21:04:54.108][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:04:54.109][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:54.110][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:54.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.112][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.113][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.114][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.116][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.117][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.118][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.120][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.120][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.121][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.123][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.127][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.128][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.129][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.131][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.132][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.133][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.135][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.136][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.137][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.138][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.139][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:54.140][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:54.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.142][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.143][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.144][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.146][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.147][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.148][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.150][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.151][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.152][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.167][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.168][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.170][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.171][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.172][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.174][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.175][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.176][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.177][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.178][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.179][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.181][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.182][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:04:54.183][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-12 21:04:54.184][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:54.185][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:54.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.193][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.196][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.198][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.200][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.201][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.202][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.204][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.205][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.207][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.210][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.211][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.213][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.214][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.215][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.219][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.220][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.222][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.223][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.224][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.226][ef$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.228][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-12 21:04:54.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:54.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:54.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:54.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:54.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-12 21:04:54.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-12 21:04:54.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-12 21:04:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.255][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.264][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-12 21:04:54.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.268][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.277][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-12 21:04:54.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-12 21:04:54.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-12 21:04:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-12 21:04:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-12 21:04:54.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-12 21:04:54.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.321][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.330][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-12 21:04:54.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-12 21:04:54.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-12 21:04:54.339][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-06-12 21:04:54.341][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-12 21:04:54.342][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-12 21:04:54.349][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-12 21:04:54.351][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-12 21:04:54.352][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-12 21:04:54.353][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-12 21:04:54.354][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-12 21:04:54.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-12 21:04:54.356][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-12 21:04:54.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-12 21:04:54.358][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-12 21:04:54.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]

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

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

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

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

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn0.9600.0533.051
LipidmapsStructureEntry0.1260.0040.129